Well, if you have an EFI bike with a stage one, sounds like they leaned it out on you to meet EPA requirements. Another possibility is if you had an exhaust put on you may have a leak and it's sucking air and igniting the exhaust gases.
I'd called them to let them know about the popping. He asked what exhaust I had and I told him V&H. He said that was normal for V&H, but to bring it in and he would have a tech test ride it.
My dealership tunes these systems everyday with no 'pop'. The only issue comes from overly open systems attached to mild builds. The normal VH system is not a problem.