I've had an issue since CS2...
Are you saying you've been experiencing these problems from AI 12 (CS2) on (including AI 13 and 14) or that you're having this problem specifically in AI 12?
If the latter, have you updated to 12.0.1? (Although not specifically listed as an addressed issue in the 12.0.1 update, it might have bearing.)
I'm currently using Illustrator 13.0.2, but it's been an ongoing issue for me since the original CS2 and all those updates.
There was a documented bug in CS2, I think it got fixed in CS3, where if you had an object behind your masked group that was the same as your mask, it would get absorbed into the group and replace the mask that was there (along with any attributes, stroke, fill, etc... that it had)
I reported it here, but I can't find my post (due to the brilliant search function on the new forums)
If that sounds like what you're seeing, get to know your appearance panel and put all the attributes on the mask itself (which will put them at the bottom of the group) instead of layering identically sized objects.