Mine did the same thing on my 09 12SCG. I went and downloaded the newest version of ECMREAD, and got the latest .xdf files.
I then uninstalled my old version of ECMREAD, and re-installed, then rebooted my computer and everything worked fine.
I uploaded the stock EEPROM, then turned right around and downloaded it back on and it all went well.
I then tried playing with the maps and turned off my servo since I am not using it anymore. It all took, because I get no check engine light, and the bike ran different. In different, I mean worse, so I re downloaded the stock maps leaving the servo off, and everything worked well, back to normal.
I don't know if you will gain much with changing the maps on the 09's, they run much richer than the earlier models and also have more tuning cells. If you do come up with something, please share with the rest of us.