More and more interesting... What about real time tuning ?
I'm starting to think your AutoProm get categorized as chip programmer so it might not be in real time tuning. Is it ? I'm not sure what would be going on with ALDL tho. I really hope I won't have to buy an AutoProm to test all this but I might have to :P
Any chance you have a regular ALDL cable as well to try ?
Anyway the debugging log should help as well.
EDIT: WAIT! Does the AutoProm does the chip programming, real time tuning AND ALDL all with the same USB cable ? If so, I'm pretty sure I know what the problem is...