I did the same thing when diagnosing a high idle that was slow to return to normal. I disconnected the AAC and the idle was very consistent - the only problem was that it did not adjust for any loading conditions which made the engine almost stall if the electrical demand was high. I did not experience any problems with hesitation or cutting out. I don't see how the AAC could affect in the way you describe, unless there is a wiring/connector problem that is shorting out.