[Endoperez]

What kind of fights are affected? Early battles with no/just few spells, castle fights, late game fights?

Even one buggy spell or unit could be enough to cause incorrect replays. For unit to cause it, it'd probably have to have some special ability.
It can happen with Windows XP, at least. Has anyone experienced it with other OSs? Thejeff, what OS did you have it with?

Try sending the turns in which this happens to Illwinter. If you could send both the turn before it (both .trn and .2h files) and the result, it shouldn't be too hard to figure out what happens. You'd generate the turn and view the battle, compare the log files and examine where it goes bad.