Always look to what was recently done. This issue could be an intake leak. Start the bike up, let it idle, and spray something like wd40, or even water all around the intake seams. If engine idle changes, that's the problem...Also, if that's a fly-by-wire throttle, it could be bad. Your bike should show you codes of what might be wrong. Your service manual will tell you how to read them...
The Dyno-Jet Power Commander may not be correctly mapped for your configuration.
Don't force it, get a bigger hammer.