Unfortunately quite often poker site support will automatically give the "we can't support 3rd party software" response whenever they see other software mentioned, even when the error is in the hand histories written by their software. Personally I tend not to mention PokerTracker in cases like this. It sounds like you've made them understand this time, though. If you hear back from them please let us know.
The problem with tournament types could be affected by the same issue but if you
compress and attach a few example HH files to a
Support ticket and tell us what the types are then we'll investigate and see if the rules need to be improved.