I tested out some short clip exports, various lengths from .5s down to .1s and they all worked absolutely fine on my system. Same length in samples, all in sync with the original, spot on. I even changed to the directX drivers to see if that messed it up, but nothing made it fail! Tried it at the start of the project and a few minutes in, tried with real-time and non-real-time, still nothing fails.
I have ‘Deactivate External Midi Inputs’ and ‘Update Display’ checked for export.
As a suggestion, you could ‘trash the preferences’. You’d have to search to find out how to do this, I’ve never done it personally. Finally, perhaps a re-install, but I honestly can’t see why that would help.
My other suggestion is that maybe it’s something to do with the soundcard latency reporting, perhaps try another sound card to see if that works. Or check your drivers are up-to-date.