Yes, I also noticed this problem... and it doesn't only occur when you're DS, the opposite happens when you're LS (for instance, Atton's alignment will drop down a notch toward DS). I've finished the game twice, once as LS and once as DS, and both times I encountered the same bug. It's not a permanent change though, cause every time I'd level up, Atton's (and whomever's) alignment would get right back up (or down) to where it should be.
But yeah, kind of annoying. At times I was wondering if I was losing influence without being notified.
It doesn't necessarily revert right back to where it was originally though. It only slips a bit... and like I said, as soon as you'd level up, the alignment would get back to where it should be.