Hi. I've done a LOT of FI engine tuning with autos and from reading the description of your problems, it's very likely your unit was bad and that the replacement one will work just fine.

P.S.- Installing and using a PCIII does not automatically void your factory warranty. The fact is, they are sold and installed at H-D dealerships all over the country.

 

I would think that if you have a problem like this you could try running a zero map and see if it still has the problem, with a zero map it should be like the PC3 isn't even there. If you still have the problem unplug the PC3 and if the problem goes away then it's the unit. Yes a new unit can be bad.