To add a few words, you got the beginning and end to match, and the middle is still off?if I fix the delay at the end, in the middle there is still a delay.
It's very unlikely that the clock signals would change within one performance. They almost always go their own way consistently.
What could do that...?
Now you're into supernatural territory. I have no good answers for that one. I could make something up like the drive filling up caused one computer to slow for the first half of the show and then a humidity increase caused the other one to start dropping samples.
Koz