You could see if anything here would help:
http://www.infinite-interactive.com/forum/showthread.php?522-How-to-run-WBC-series-stably-on-modern-setups Do you notice anything in particular when it freezes? Like your hero finishes doing something, a certain sound plays or whatever when it freezes. Did you change any settings after installing and if so could that be causing it? It might be possible something the game relies on is corrupt or didn't install correctly. Have you tried reinstalling it? Did you apply any patches after installing?
Do you know if it froze the same way before you fixed the invisible units bug? How did you fix that by the way? I thought that compatibility settings usually fixed it but I've seen solutions that were a bit more involved. Could that be the problem?
Is it possible anti virus software is causing you grief? You might also check to make sure a Windows feature called direct play is installed and working, but I'd be surprised if that was the problem in this case.
It should work as far as I know, so I'd be inclined to think something isn't quite right with your setup/computer. (I might be wrong there, but I have gotten the game working just fine on a similar system.) Although you've already dealt with any common problems I'm aware of.
I'm sorry I couldn't be more help but it's hard to know what might be going wrong with so little information and the fact I've never encountered this issue before. Hopefully you'll be able to track the problem down.