AA3 = Atomic Amplifire 3?
I'm not familiar with that IR loader. You have to be careful with some of the implementations, they sometimes don't get it right or are peculiar with the IR.
One thing you have to watch out for is when you upload to the AA3, does it convert the wav IR at all? Or how does that work? They may do a minimum phase transform to remove any silence at the beginning of the IR.
On your PC, the IR loader may not be doing the same thing so you may be listening to IRs with silence at the beginning (which changes the response completely) or they may be truncating them too short... or any number of things they could do wrong. Though just looking through their website, PULSE IR loader seems targeted for cab emulation.
What's your workflow?
Maybe stereo processing differences?