I'm probably the only person that will respond to your post!
I don't know how you expect to get any help considering the disorganize way you have provided us with information about your system. Your post isn't atypical. If you go through this forum, you'll find hundreds of posts without any replies.
Since FMS runs perfect on my computer and countless others, I doubt that it is at fault. The models crash because of some sort of conflict (interrruption) between the interface and the program. Second why would you need to disable the COM ports in the BIOS? If you aren't using them, they can't possibly conflict with the program or your method of interface.
You might describe how you're communicating to the program: USB, gameport (analog), serial port, or parallel port, and the controller you're using: TX with interface cable, Joystick, Gamepad, or whatever.
With some specific and logically laid out information, I'm sure you get some help.
Al