Alright, I did NOT rotate my cartridge, only the compressor housing. This could be the problem, though I'm no expert on the internals of a turbo. I would say one of your best bets at the moment would be to call Turbonetics and ask them if it is O.K. to rotate the cartridge along with the compressor side. You might have found your answer, but I'm not positive.
Thanks for the compliment, though I don't have a cold air intake on my car. You can check it out here though, and tell me if this is the one you are thinking of? I have what might be called a semi-cold air intake, but my intake is not in the fender like normal CAI's.