After I press "start", the main menu appears and then starts scrolling down rapidly as though I were holding the down arrow. It's like what happens on some consoles when you boot them up without making sure the controller's analog stick is centered. The only input devices I have plugged in are a trackball and keyboard. Suggestions?

Check the config menu hasn't detected the trackball as a joystick.

Perhaps it detected a gamepad and the analog stick isn't dead center. (Or where the game expected it to be.)

I play with a game pad and at the menu I have to circle around the pad every time I start the game or it does that. Its like its testing the axises but it straitens right up once I do press all directions. Its a little weird but knowing the trick fixes it and it isn't a big deal.

This only happens with the XBOX 360 Controller for some reason. It happens in games like Sonic Mega Collection Plus, and a few others as well. (Older EA Sports Games) Has to do with the controller reporting an odd axis.

Well I have what sounds like the identical problem as the OP and I'm not using and XBOX 360 controller.

Posting which controller you have would help me to solve your issue. There are work arounds for this problem.

I'm just using a ps2 controller through an adapter and I don't really consider it a problem. I just circle the pad and it works perfectly. It doesn't interfere with anything.