I've had similar problems with drums. Not any real timing issues but drum tracks that get frozen somehow and won't overwrite when changing styles or realdrums. Nothing to do with freeze settings but somehow frozen behind the scenes.
I've never quite figured out how to reproduce it, or how I've fixed it when I have managed to. Some songs I couldn't fix and had to create a new song and copy the chords over to start again.
The only thing I do know is this will happen after I've added a drum intro in song settings or changed something in part markers.