Everyone I know who records audio regularly in Logic Pro has this problem. I work on a few different combos of logic interfaces, computers in different studio setups and it happens on all of them.. Some days, it hardly happens at all, while other days it might happen 20 or 30 times in a 3 hour session.
It's been going on pretty much in all versions of LPX. I work with union musicians who are used to working in protools. It's very frustrating to have a really great take recorded, only to have it play back out of sync. You can try to line it up to make it right, but the chances of getting back to its recorded position, or even within 10 or 15 milliseconds, is slim. Rather than breaking down the flow and spending time discussing if it's a little ahead or behind, we generally just throw away what would be a good recording.
I have not experienced it during the initial recording of the multi track, which I always start at 0. It happens when we start to do the "fixes" with individual overdubs, even if the overdubs involve multiple players and their tracks. It may be if you start a recording from 0, it stays right. Or it may be that it only happens to rather short takes, or while you move to different locations to do the punch ins for overdubs. As Jasonhou mentions, it is tempting to move the recording portion of recording projects to protools and do the mixing in Logic. But I am a die hard and keep hoping the next version will fix it so I can keep the entire project in the same workspace.
Anyway, I'm hoping Apple will get to the bottom of this soon.