I’m sure this will turn out to be something exceptionally stupid on my side, but here goes…
I recorded a session about a week ago using Ardour 3.4 (on Fedora 19 + CCRMA), then I edited it over the course of the following few days, as I had time, using Ardour 3.5.14 (on Fedora 14). After several editing sessions, A3 seemed to be getting somewhat more crash-prone - a couple times just opening the session and hitting the Zoom-to-Session button was enough to make it seg-fault - but otherwise things were going fine. Tpward the end of editing, I decided to add some fader automation points so as to avoid an audible click that had occurred right before something I wanted to keep. The click waveform looked quite distinct, but just to be sure I had the right place, I positioned the play head just before it and hit play (indeed it was there), and then just after it (no more click). With that verified, I added automation points to set the fader at -inf some time before the click, and two more just after it, one at -inf, and the other back at 0. Very routine - I’ve done this sort of thing many times before.
When I played this, the automation worked - the fader moved - but to my surprise, the click stayed in the output. At first I looked for obvious errors, such as forgetting to set play mode on the fader “track”, but didn’t find anything. I experimented with sliding the automation points around in time, and found that there was an offset of about 200 ms between where I thought I was putting the automation, and where it actually seemed to be taking effect. Exiting Ardour and re-starting didn’t help - I tried it several times.
I’ve tried reproducing this in a new session, with no luck – it works fine, of course! 
I guess if I never see it again it won’t lose any sleep, as this was one of the last few edits I needed to make on this session. But with my luck…
Any ideas how I could troubleshoot this? Is there anything in the .ardour file that would be relevant?
Thanks!
Don