I'm not sure I understand your problem. My best guess is that you think trim should be neutral? If that is true, that is not correct. Trim will not be neutral in most planes. Is your plane flying normally using Combat Trim without looking at trim settings?
If it is not flying normally, first make sure that the rotary dials on the base of your CH stick are centered. You should not use these dials as trim. They should only be used if your joystick spring centering mechanism is not working correctly.
If you have trim mapped to your controller, particularly an analog control like the mini joystick on the throttle, you have to cycle it also when you calibrate. I hope you have calibrated your controllers in the game. Try removing any mapping of trim and see how that works.