Mine started with Triumph's TOR canned tune. Doubt that is the problem.
I hate to say it, but you may have to take it to a Power Commander tuner. It could be a problem with the unit itself and the only way to determine that is with another one.
The only do it yourself diagnosis tool is to load the TuneECU software into your laptop and plug into the bike to determine what the parameters are and what's going on different with an without the PCIII. I'm not suggesting altering the ECM base program, just use it to diagnose. If this is over your head or more than you want to tackle, take it to a tuner. It's money well spent anyway, you can get a custom dyno tune while you are there.