Load up the the winIPAC utility,look up on the menu bar and click mode,click panel designer.Are all your buttons and joysticks showing here? If not, ad them in with the little box on the left.use the arrows to switch items(p1 start,p2 start,etc).Set up your virtual panel exactly as your real panel is setup.
Once you have you have everything placed on your virtual panel,click a button to highlight it,now look over to the left again underneath the box you used earlier.See where it says IPAC CONNECTIONS? This is where you 'sync' per se your controls to the ipac. Go through all the joysticks and buttons you have placed in your virtual panel,and set the switches accordingly.so if you highlight a player 3 button on your virtual panel to the right,and on the left in those little boxes that button is binded to ipac p1 sw3 for example,that will be an issue.Keep your eye sharp to the p1 p2 p3 p4 boxes when setting the switch numbers.
Map all the buttons to the correct IPAC connection,and save the control panel,I suggest you back it up somewhere safe.After that go back into key assignments editor,up in the mode menu,and start removing all the double bindings.This would also be a good time to remove ctrl,alt,and shift as primary buttons because they cause alot of issues.
I hope this helps.