1) Electrical Noise. BRP put out a tech bulletin to ground the coil pack (on left side). The electrical noise can interfere with the TCS computer CANBUS communications, resulting in missed / wrong reading. This gets you stuck in some gear or the "E" on the dash. My GS has green 10AWG wire under the tupperware tying everything together that could be - coil, engine, frame, back to rear fender frame, etc.
2) Gearbox position sensor. HUGE pain to replace, I have a big thread about replacing mine here on the forums. This causes the transmission icon to light, stuck in gear, in WRONG gear (says 2nd but in neutral), etc. Mine was worn out, the center shaft flopped about. About $125 replacement, watch a couple videos on getting belt off by jacking up bike and removing rear shock bolt - instead of messing with alignment screws.
3) Stripped shift lever (rare but mentioned here on the forums)
4) Shifting solenoid not grounded and/or not fully engaging (showing wrong gear; trans light; etc.). Solenoid puts out a big wave of electrical noise. Very randomly could interfere (based on my reading).
5) I think there was a software update (2010??) when this was happening a lot. Would need to take to dealer to check software version.
If you are a DYI person and take off the tupperware on the left side, also check the torque on the front sprocket (16mm?). Should be 110ft/lbs. Mine was finger loose, never had the service bulletin work done! Manual says 95 ft/lbs, it comes loose and the bolt threads started wearing. I used blue locktite per many forums' recommendation. New bolt is like $10 from cheapcycleparts.com.
When my 2008 GS started down this road I was on all the forums researching!! Was getting tired of stopping every hour to pull key to get TCS computer to reset :banghead: ...
GL!
Steve