You said you just replaced the motor... sounds like you have it a few cogs off on the gear on the motor shaft. You may be able to loosen the motor enough to move the wipers to the proper parked position (without turning the motor shaft) and then put the motor back in place. Then you should be back in sync.
Most likely you have a screw floating around in the case on or under the board. Or maybe a cable just barely connected or loose board. Check carefully w/ a flashlight for these things. One thing you could try, take the new sound card out and see if it still locks up on you, it may be the sound card is defective, causing your problem. The other possibility is a crack or bad solder connection on the mainboard.