I think you just have to never press the button that shows the replay for every ship. Otherwise, with 100+ ships, you will see the replay 100 times, or something, IIRC.
Last time that happened to me was like Version 1.49, I reported it to MM at length, and unless I'm mis-remembering, I think I've been afraid to press that button ever since.
As long as you press the other play button (and don't do PBEM/PBW with multiple computers without loading the previous turn first), I don't think you'll have a problem. Or at least, I haven't had that problem since way back then.
PvK