interesting I just had something like that which seemed to be script related...
big battle with spawned armies and some things that should happen via script after battle; worked fine on autoresolve and fine losing battle on battle map by exiting battle early on, CTD'd regularly on trying to return to strat map if you actually played the battle out for a long while - win or lose. Improved after moving some of post battle scripting off to end of turn monitor.
do seem to be having some memory leak type symptoms with Alex.exe - eg bits that should work fine, don't after CTD and re-start of program. Never had anything like that on BI, do you know any more about which .exe's are effected and if scripts are a contributory factor?