Test tone … is an x86 bug …
Im am sorry, my keyboard is a bad one 
Hopefully you understand me anyway.
No, I don’t.
I have a track, which contains a sweep test tone. There is another track recording the signal from the 1st track. During the recording you hear a click when switching the focus from the main window to the mixer window and vice versa. I will now switch the complete system from stable to testing and then see what happens.
Clicks caused by using the GUI indicate system-level issues, not problems in Ardour itself. They can be caused by the kernel, by video drivers and a few other things. They are all hard to fix.
I know, of course, I do not think that ardour is causing this in any way. Since there are distorations in the monitor ouput when starting jack without ardour, this is clear. In the whole thread I described what I tried to fix it but I still don´t give up.
I switched my system to Ubuntustudio. It works without issues. It is not that comfortable than Gentoo e. g. i need to download and build the hdsp firmware by myself but that is not a big deal.
On my backup computer i will stick to gentoo and continue to find the bug and fix it. The fist step will be to clone the Ubuntustudio kernel and let it run within the gentoo system. If this does not help, I will continue replacing all application packages step by step.
But anyway the primary issue is fixed because I have at least a working system.