What kind of negative effect? I've noticed there is a pronounced pitch up with flap extension if CT is on.
Exactly the problem. With your flaps extended, you have greater lift. Combat trim only (I believe) looks at speed. So flaps give you more lift (but also increases drag which brings your speed down a bit), combat trim sees a drop in airspeed and trims your nose up (to take the back pressure off your stick) because it thinks it needs to keep your nose up to adjust for the lower speed, and the result is you balooning into a steep climb. At very high or very low speeds, the CT has (or causes) trouble.
If you use flaps during landing, you should turn off CT and trim manually. Otherwise, the chances of balooning up and stalling increases and you may very well pancake onto the runway.