If you're using a flite yoke or flite stick that has a pitch trim wheel or lever, check that trim wheel/lever to see if it may be in full nose down trim.

The auto pilot over rides your control yoke & trim until you disengage the auto pilot.

Steve,

Try recalibrating your yoke.

Art

Check this from the FS9 autopilot help;

Don't attempt to manually control the aircraft with the joystick while the autopilot is turned on. If, for example, you select Altitude Hold mode and then try to hand-fly the airplane, the autopilot will compensate by running the trim. This situation can lead to several problems in the real world, especially if you're flying in the clouds. For example, upon disengaging the autopilot, you could find that the autopilot had run the trim all the way nose up or nose down and have a very hard time maintaining control of the airplane, or the autopilot could disengage itself after hitting the trim limits. You might assume that the autopilot is still on, release the controls to unfold a chart, or tune the radios, and enter a spiral, stall, or other unpleasant condition before you figured out what was going on.

Maybe?