brother, u said it the right way. It's the actual trouble I'm facing with my GS. It is like when u choose to ride on constant speed i.e. no acceleration, the engine does not sustains its momentum and u feel like being in a lag.
What I did to help the situation, I took the bike to dealership, and the mechanic there made the mixture lean. the lag somehow vanished a bit but acceleration and the powerful feel also went away. I then myself turned the mixture screw anti-clockwise one rotation (360?). Acceleration is normal now, but now the lag or minor missing dtuff is haunting me again :S
do tell me how did you cope it ? and was it something associated with the break in period ?