Weird phase issue when bouncing tracks

So today I was bouncing tracks from my old pc to my new pc- everything 24bit 44.1k mono and when had everything up in cubase, at random points the overheads and guitars would pop in and out of phase. I'm not sure what is causing this seeing as how everything has been slipped to the grid in a prior session and sounded fine.

I did the same with some drums I programed in fruity loops. I would solo snare/kick on separate tracks and use trigger just to see how it sounds. I'm getting the same problem. When I zoom in to the transients as far as I can, I would line it up and scrub farther down to see that the tracks would find themselves milliseconds before or after the original print.

Not a huge problem because I am planning on buying SD with tax return $ and it hasn't effected my recent sessions- but I still find this odd with the old session and the overhead and guitar thing.

I can post screen shots or clips if interested- I'm wondering if any of you guys have has this problem?

Did a search and couldn't find anything. Idk...