Well what changed? What tuning features were you using on the HU? What tuning features are you using on the computer? Do they have similar features/options?
The center/sub connection is split between the center channel and sub. That could cause weird sounding problems if you are trying to run center channel frequencies to a subwoofer.
Is there a way to run that card in 4 or 5 channel stereo mode rather than 5.1 surround mode?