I've been noticing this a lot, recently.
I do drum covers on YouTube.
I import and a song from iTunes — drag and drop into the project, and then I record my 8 mics that are interfaced through my Focusrite Saffire Pro 40 at either 512 or 64 samples. It has happened at both.
I record it as I want, stop, and save. Then, when I go to playback, it's slightly out of sync. It does this 1/3rd of the time, pretty much.
I'm on LPX 10.01, by the way. I think I may have had this problem with Logic, once before. Literally, one time.
How can I fix this?