Button issues in Candy Cab

[Sky Zero]

After coming home from work today and wanted to get some work done on my candy cab project. Looks like I'm running into a lot of issues regarding the buttons. For reference, I'm talking from within Street Fighter 4. Original problem was that buttons 5 and 6 wouldn't register together on Player-2. Now when I press button 2 on the Player-2 side it causes the button 2 on Player-1 to register. Also ran into another issue where pressing Button 4 on Player-1 seems to register as a throw now (which is usually done using buttons 1 and 3), instead of just a light kick.

Button Layout:
123
456

Currently, buttons 1-3 were already installed in the cab and are connected via a harness. Buttons 4-6 are wired according to the J-PAC instructions on adding additional buttons with the ground being daisy-chained.

Checked WinIPAC and made sure the buttons are not mapped to the same keys. Using the test mode, buttons seems to register correctly. Loaded up PPJoy and the buttons are set correct for both virtual joystick devices. One thing left to try is to re-install the game and see if that helps. Just in case it isn't software related (game, keyboard encoder, etc.) is there anything I could check hardware wise to make sure everything is the way it should be?

Feels like I keep running into more and more problems those closer I get to that finish line. Any help would be greatly appreciated!