My 07 is currently at the dealer for this exact problem.
In my case the problem happens about 80 miles/1.5 hours into the ride.
I notice that the throttle has a "dead" spot in it, most noticable when taking off from a stop.
The first few degrees of throttle rotation is no problem. The next few degrees ether it starts missing badly or feels like it wants to drop to idle. I can twist the throttle a few degrees in each direction with no real effect in engine rpm. The next few degrees its OK again.
The last time this happened I stopped and checked the TPS using the diagnostic mode, everything looked fine, no skips in the reading.
Shutting the bike off and restarting it clears the problem.
I have a Power Commander, the problem exists if I have it connected or not.
I am not optimistic about the dealer solving the problem.
I will let you know......