Weird gear selection problem - 2005 R3

Since the problem showed up with the addition of the new clutch lever I would guess you have some kind of an adjustment problem. First off, these bikes are fussy when it comes to clutch adjustment. There needs to be at least 2 mm of freeplay in the clutch cable. If the freeplay isn't there you could wear out the clutch lifter piece and shaft which prevent you from fully releasing the clutch. Second thing to check are the new levers themselves for full arc of travel. Not enough travel will cause the clutch plates to not fully release giving the condition you have. If you can't see any problem, swap the levers back for the original to see if things get better. You didn't happen to remove the belcrank from the clutch lifter shaft? If so, did you put it back in the proper position?
 
Had the same issue with my 05. "managed" it with Turbo suggestion and lived with it. My '12 does it as well some times. If you really want neutral. Get there just before the complete stop. Good, bad, or indifferent
 
Had the same issue with my 05. "managed" it with Turbo suggestion and lived with it. My '12 does it as well some times. If you really want neutral. Get there just before the complete stop. Good, bad, or indifferent
Cool - good to know. I'll try that this week and report back. Thanks for the useful info guys.