If there are any MIDI FX in the project, anywhere, try removing them (disabling is not enough). There is a bug with MIDI FX that causes some or all of the next measure after the loop region to be played back on all passes after the first. Depending on what's in that measure it can screw up the timing.
EDIT: This bug is a pet peeve of mine because I need MIDI FX in a lot of projects while tracking to block CC123 from my old Roland RD-300s. Fortunately, I just got an RD-700NX, and it doesn't send CC123. Will be retiring the RD-300s as soon as possible!