I have had this problem, and it is really annoying when it comes up.  Occasionally, My joystick slider will stop controlling engine #2, and no matter how many times I press E+1+2, the engine will refuse to be controlled by my joystick.  

Please don't tell me to register FSUIPC and use the "Control all engines" command or whatever FSUIPC uses, because I paid $35 for the product, and I don't want to pay an extra $20 just to get it working properly.