Custom battles currently do work. Sorry had to Edit my post here- custom battles were broken for awhile and I hadn't tried one yet since I'm back to see they are fixed.
Battles from campaign should work... with all the patches and hotfixes it is actually remarkably stable and after 20 test campaigns I only had a crash before turn 100 once and most campaigns ran 200 to 300 turns no problem.
Also I've never had a crash playing a battle yet- some silver surfers sure but not crash to desktop.
Run SS6.4 setup again and try reinstalling from that point... it should work. Everyone else that has reported issues eventually figured it out by doing install a couple times and making triple sure everything is in the right order and files copied into data file- not extracted directly into data. For some reason you have to copy the patches into a separate directory then copy into the data folder. First time I installed patches I didn't realize this part either and just extracted directly into data folder and crashed.