This is resurrecting a bit a dead thread a bit, but i was having a similar issue. I noticed my files were all sped up after closing Ardour on my Kubuntu system. But i noticed it wasn’t just the audio file, it was every application after closing Ardour was sampled strangely, Firefox, VLC, Games, etc. A restart fixes it but i wanted a better way.
I tried reloading alsa, and a few other things locally but couldn’t find a fix to get it back to normal. So i decided to try a workaround. I loaded Ardour, started a new session, and set the sampling to 44.1 instead of my preferred 48 for projects. I Let the session load, and then closed Ardour. My computer was back to normal after that. So something curious about Ardour not setting the audio back to how it was before the session started. Unless I hear a better fix, i may just keep doing that.
Run my sessions in whatever sample i need and then when i’m done, restart Ardour one last time, and set the sampling to the usual standard 44.1 to straight it out for everything else.