Use the CTFJ to set all 3 axis to 100% X, Y and R i.e. defaults, and make sure the Center box is checked for each and dead zones are set to minimum 3, then use the windows calibration link button in CTFJ to calibrate the joystick in windows, then press the centring axis button in CTFJ (hold your mouse over each button to see what each one is) and then re-calibrate once again in windows again to make sure it is correct with CTFJ centering on. All axis should now be centred properly.
Re-calibrate in AH with CTFJ running, and then see if the graph is giving smooth output, if it is then check if auto climb etc work now. As a tip when calibrating the throttle in AH, when it asks you to move the throttle to the limits, stop it only just short of each end so that ensures wep will always engage and idle is definitely idle.
The graph for stick setup in AH should be smooth on each axis with no big jaggies, it it's still spiking you have either a dodgy pot, or the gameport itself is causing the problem. Sometimes just removing the gameport in the devices list, reboot and let windows re-install it again should fix it.
Lastly in the Stick controller listing in the Control panel in Windows, make sure that the box for Poll with interupts enable is un-checked.
Can't think of anything else to help you.