Chris, it zeroes itself every time you cycle the power. I understand your question, and you do not have to be concerned about the FAST unit being confused where the IAC actually is. It rams the pintle into the seat every time it gets turned off so it is at zero on powerup.
Is the IAC count really high when the idle speed is too low? Does it sound like the IAC is wide open? If it is, and the idle speed is too low, either the TB is dirty and not letting air flow around the blades or perhaps there is a fueling problem causing the idle issue.
If it doesn't sound like the IAC is wide open, something is possibly wrong with the IAC motor itself, the wires that run it, or possibly the FAST unit itself. It's not a common problem to have a failure of the IAC driver, but it happens.
Check continuity from pin A to B on the motor, and then from C to D. Each one should be about 50 ohms. This is the resistance of the two coils in the IAC motor. Make sure that pins A or B don't have ANY continuity to pins C or D.