Could the engine be going into Limp Home mode?
The Sender for the 2-stroke oil level on these engines is prone to failure fooling the system into thinking there is only a limited amout of oil in the tank.
The ECU then drops the max revs down to 2500.
In the past I've hard wired the plug for two of these sensors into 'Full' mode when they gave up the ghost. They are a brass tube with simple array of reed switches activated by a magnet on a float in the tank. Cutting the plug off the sensor and looping the wires together is easy to figure out if you open up the sensor to see which wire goes to the top reed switch.
Both I opened up were a mess inside after moisture had got in.
Suzuki reccomend they are changed as a service part every other year, only they are a couple of hundred quid each.
On the other hand its probably something completly different.