Direct Pad Pro with Genesis Controller

I understand that Direct pad Pro may not work with the Genesis controller due to a problem with the LPT1 port on newer mother boards and chip sets. However, I was wondering what kind of problems would it cause. I am trying to work on a reason why my set up isnt working. Im not sure if its due to interface I built or if its this compatibility problem. Everything seems to be ok right up to the point I go to configure the controller. Number 2 and 3 buttons seem to be always pushed while the joystick goes crazy. It wont allow enough time to swirl the pad and then center it. It just jumps from Swirl, push a button, Center, push a button to it being calibrated before I can push a button. I first tried it on a 750 Athalon running ME with DirectX 8 and then on a !.4 Athalon T-Bird 98SE with DirectX 8.1 and both had similar but not identicle problems. Any help or suggestions? Thanks.
Try going into BIOS setup and changing the parallel port mode to SPP, if it's not set to that already.