I noticed a smiliar behavior as well.
I jumped into the third, Caucasus - Airfield Takeoff and Navigation Quickstart mission. Took off, followed the first few waypoints with little thrust and then pushed the throttle all the way forward after I flew over Sukhumi - Babushara till Beslan.
Upon landing approach at Beslan I noticed the aircraft/engine was performing differently depending on the nozzle degree. I crashed, fell out of the sky, right after that when attempting a SL.
Perhaps we are really missing something here due to lack of knowledge with the Harrier.