My 03 Chopper has been doing the same thing and that is exactly how I described it, "a hick up!" The guy that has been working on mine is pretty knowledgeable and has adjusted the carb for me in the past. Anyway, when I mentioned it to him recently he said, "before we get to far into this and get real complicated when's the last time you checked or changed your spark plugs?" I'll let you know what happens, its been over 100 degrees everyday for more than a week so I haven't been real compelled to get out there and try it or ride it!
I know it sounds simple but one other time I had a really odd problem, this time it was at the Big Dog dealer, and after not being able to figure it out and contacting BD the person at BD asked if they tried the spark plug wires. That was about the only thing they hadn't tried, they were into all kinds of shit! Guess what? They changed the wires and it was good to go! So just maybe!