Before proceeding any further I'll ask one question. Do you have a FI indicator showing on the dash. That indicator is like the check engine light on a car. It tells you the ECM is getting a bad reading from one of the sensors. If you don't have that light then read on.
If the plunger is not stuck then diagnosis becomes more problematic. It could range from the switch being bad to a problem inside the CVT. Your going to have to eliminate things one at a time until you find the problem.
Cheapest and easiest to check is a bad center stand switch. Good news is that all you have to do is unplug the switch. With it out of the circuit the bike should shift normally if there is no other problem. Bad news is that you are going to have to remove some body panels to unplug it. The plug is under the floor board cover and you have to remove that cover to get to it. Once you have the cover out of the way you can follow the wire up from the center stand to the plug and unplug it. LeDude's - Burgman Center will give you instructions on how to remove the floor board.
https://sites.google.com/site/testburgmancenter02/
Since you will likely have the bike on the center stand when you do this you can just test it there without having to ride it. Start the engine and rev it up then try changing ratios in manual mode. If they change then the switch is bad.