I'm not sure if it addresses this particular issue you are speaking of, however, many people have put a PCIII usb on their 06's and claimed it made throttle response way smoother.
That was my experience. I bought the PCIII specifically for that reason. If one is using the bike for commuting or relaxed touring it's no big deal. If one is trying to carve corners more aggressively the on/off jerkiness is a major hinderence IMO.
FWIW, with the PCIII (stock map) the bike also lost the breathless feeling it had rolling on hard from low RPM and only suffered a ~2 mpg drop in fuel mileage in the process. A damn good tradeoff if ya ask me. Shame you got pay extra to get it the way it to run the way it should have shipped from the factory though.
I have only one complaint about the FJR. Too much drive train lash...
The lash you are experiencing is due to the choppy on/off FI characteristics. Spring for the PCIII, you'll be glad you did.