There are a few things that could be causing this, dirty sensors, dirty filters, dirty throttle body, dirty MAF, or a bad tune. :/
Firstly did the tune ever perform right? as in did you ever see what you are seeing out of the canned tune with the performance tune loaded? If it did then I would bet it is one of the sensors or throttle body that needs to be cleaned, if it never did that good, then I would guess that it is a problem with the tune itself, which Bill can and will fix for free (to the best of my understanding).
Your answer to the above question should determine your best course of action, and even if it is just a bad tune, it can't hurt to clean out your engine parts
. hope this helps.