Also (in case you’re using Windows) you could launch Task Manager, then select the Processes tab and CPU (make sure the CPU arrow is pointing downwards).
Now keep an eye on the CPU usage and see if any particular process comes higher up the list each time you hear the beep.
There’s probably something equivalent for the non-Windows OS’s but I don’t know what it’d be.
I tried to connect both my electric guitars: a Squier Deluxe Stratocaster and a Jackson Dinky JS-30 and I could hear the beep with both.
Also the Jackson has humbuckers so I guess using single coil or humbucker pickups doesn’t change things too, could I be right?
I tried to use this balanced jack cable which should also be stereo but unfortunately I still could hear the beep… 
Unfortunately I can hear the beep even just by powering the audio interface; regardless of the use of a specific operating system or an external power supply, this makes me think processes are not involved…
Can you load Windows and open Device Manager? You’ll find your sound card listed under Sound, Video and game controllers. Select your card and click its Driver tab. If there’s a button saying Disable, disable your card temporarily and let us know if you can still hear the beep.
Honestly it really is. I have never seen a single DI box that came close to the amount of noise injected by those (It is possible I am remembering the wrong Behringer DI box that looks exactly like the one referenced).
Potentially, I would see if I can borrow one, but it may be a ‘masking’ more than a ‘solving’ depending. The reason for those is that Passive DIs will result in a lowering of signal, not to much unlike the pad switch on that DI box. That being said, the typical rule of thumb I give people is “Active Pickups, Passive DI/Passive Pickups, Active DI”. Essentially if your instrument has a battery in it or plugs into the wall, it isn’t a horrible ideal to stick with passive DIs in most cases. If it doesn’t, then you need to use an Active DI.
This isn’t to say that you can’t use Active DIs on Active Pickups, but it will depend on the quality of the DI to an extent and capabilities on whether you get issues, passive just tends to be safer if you don’t want to think much about it. The Radial J48 or Countryman Type 85 are some of the highest regarded Active DIs most people wouldn’t blink at using on active pickups in most cases, but I still carry around some JDIs and ProDIs variants as well as some cheaper Whirlwind IMP etc. passive DIs.
This bit of info is unrelated to this as you have now tested both, but I will say single coil pickups are more prone to interference, and in fact this can be a major issue in venues that run induction loop assisted listening systems as you can pick up the signal on a single coil pickup, causing feedback if the guitar is fed into that system. That being said, I will again reiterate that it is unlikely to be a significant contributing factor at this stage since you tested humbuckers as well.
Can you make a recording of the beep and post it to listen to? Otherwise I am curious as to the results of @John_E 's question as well obviously.
Seablade
Hi Seablade - deperito left a recording here. What’s strange is that when I first listened to it, it definitely sounded like a beep but today it’s sounding more like a click here 
Ahha thanks John, I missed that earlier.
That is an odd one. I would suspect locally generated RF in that case, especially given how low it seems to be in the noise floor.
Are you by chance using wireless keyboard/mice or something along those lines?
Of course if it is as low in the noise floor it seems, my follow up question is going to be, are we chasing after something that in the end won’t make a noticeable difference and would be drowned out by any desired signal on top of typical editing removing background noise anyways?
Seablade
Hi again @seablade and thanks a lot for the very useful info!
May I ask you for exact models of active and passive DIs so that I can try to get and test them?
If I got it right for the active ones you recommended the Countryman Type 85 and the Radial J48, correct?
On the other hand, for the passive ones you suggested some JDIs and ProDIs as well as some (cheaper) Whirlwind IMP, but I didn’t understand if these are just brands or exact models… If it’s the first one: could you give me the exact models? This way it’d be easier for me to find them
Are you by chance using wireless keyboard/mice or something along those lines?
I am using wireless mouse, but in my tests I also tried unplugging them from the PC along with all the other peripherals but the audio interface… And the beep was still there 
are we chasing after something that in the end won’t make a noticeable difference and would be drowned out by any desired signal on top of typical editing removing background noise anyways?
Unfortunately I’m afraid I can’t ignore it… In fact - as you could hear in the recording - it can be clearly audible and due to its “random time persistence” the very chance is to get it in the middle of a recording, maybe right in a point where the desired guitar signal is quieter, making the beep come out clear as day…
… It’s a really annoying issue.
@deperito - what happens if you remove the batteries from your keyboard and mouse temporarily? Does that stop the beeps?
Along with pulling the batteries you would need to unplug the receiver.
USB3 ports on some computers are known to cause interference with wireless keyboards and mice, so I am curious if you are somehow getting the same in reverse for the record.
Ill respond to the OP more later, in a final dress rehearsal for a show atm.
Seablade
Generally, Whirlwind, Radial, Countryman all make respected DIs that do a good job. The Radial J series in particular is considered the better out there (J48 for Active, JDI for Passive) by many people. The Countryman Type85 is well regarded but not as often used, I think just not as many people have used it to know it. The Radial Pro series is a good cheaper alternative to the J series, at about half the price IIRC. And if you want to save more money the Whirlwind IMP2 is one of the cheaper boxes that is a solid workhorse you will find quite often used.
Going cheaper than that I would generally just recommend sticking with Passive honestly. There are budget brands such as Livewire or Rapco/Horizon that have options here.
Oh it is audible yes, but it seems to be very comparable in level to the noise floor of that recording, and generally you shouldn’t be anywhere near the noise floor of a recording in decent setups even if playing quietly, which is why I was wondering, that noise floor should be at least 40dB below your typical signal levels in general I would think.
Seablade
Same this morning. It’s weird but what I hear now is a short sequence of clicks followed by a very brief modulation of the noise floor. No beep at all any more and yet there was a very distinct beep when I first listened
I’m sure that at one time, it was possible to add something called dither to Ardour playbacks (it’s a very small signal which combats weirdness happening at the noise floor). I can’t find it any more but the closest I can get is a setting called CPU/FPU denormals. I don’t know if that’s some posh way of saying “dither” but it’s available in Window->Preferences->Performance if deperito wants to experiment with it.
[Edit…] And if that doesn’t help, please try our suggestions of removing your wifi receiver temporarily, along with the batteries frm your keyboard and mouse (and elt us know if that helped…)
I’m sorry, I did a mistake in the previous answer: to be correct I’m using just a wireless mouse, not a wireless keyboard.
Anyway I didn’t try to remove batteries from the mouse, I just unplugged the usb receiver from the PC. Given this, removing the batteries shouldn’t I get the beep anyway?
Unfortunately I’m forced to stay away from my home studio for about a month, there including PC, audio interface and guitars I use for recording… But I will do the test once I’ll have access to them again and let you know.
Of course I’ll also try that dither plugin you suggested
Thanks again for the advices.
As I wrote in my previous answer, I’m forced to stay away from my home studio for about a month, but as soon as I come back I’ll give some other DI (possibly one of the ones you suggested) a try and let you all know.
Oh it is audible yes, but it seems to be very comparable in level to the noise floor of that recording, and generally you shouldn’t be anywhere near the noise floor of a recording in decent setups even if playing quietly, which is why I was wondering, that noise floor should be at least 40dB below your typical signal levels in general I would think.
So you’re saying the noise floor (and thus the comparingly in level beep) may be too high itself… Did I get it well?
In this case may I ask you some advice to reduce noice floor regardless of the rest? Maybe - leaving the beep aside for a moment - there’s something wrong in how I set up my recording environment anyway…
Well that is a pretty loaded question honestly. To answer it fully would be a more detailed response than I can likely give in text without writing a book on gain structure. I would say it would be interesting to get a recording of you playing the guitar that you can hear the beep in to see how the noise floor level, the guitar level, and the beep are all interacting.
The single most important thing you can go though is to make sure your input gain is set correctly. Given a typical 24 bit interface, on your typical playing, you should be seeing levels around -20dBFS, giving you 20dB of headroom. LIkewise your noise floor in these situations should be located well south of -60dBFS, really south of -80dBFS would be a good indication of a nice quiet recording. but often is dictated by your environment and may not be possible for instance if recording in a bedroom studio, sometimes. That being said since you seem to be recording direct from the guitar I would hope you can at least get 40dB SN ratio as mentioned (-60dBFS Noise Floor or greater).
Seablade
I was wondering if the wireless signal from your mouse might be interfering with something else in your computer somehow - so you’d need to remove the battery to stop its signals from getting generated.
Given that the interference is noted in physically close locations, but not in another city the source of the interference being an peripheral which travels along with the computer, vs. a source such as cell phone tower seems unlikely.
No, denormals handling concerns a quirk of floating point math, it is not related to dither.
Dither settings can change distortion behavior near the digital noise floor. That should typically be well below the electrical noise floor in most setups, around -93 dB FS with 16 bit devices and around -144 dB FS with 24 bit devices. This interference is well above that level and sounds like classic interference from a high power radio frequency device somewhere in the vicinity.
but even so Chris, the mouse is a wireless device so it could easily be the mouse that’s being affected by the signal.
I guess it’ll be another month before we get to fnd out 