When watching Dolby 5.1 DVD's using Dolby Digital processing, what you are hearing is exactly what is on the disc - all that the 990 or any other processor is doing is decoding the source. If discrete effects are lacking in those cases, it is a result of the original mix. When watching Dolby 5.1 DVD's using Pro Logic IIx Movie to expand the audio to the rear surrounds, all that Pro Logic IIx is doing is manipulating those left and right surround channels to produce rear surrounds from those signals.

The Model 990 is pretty radically different from the Fosgate Model 4 you mention. The Model 4 is an analog Pro Logic decoder that works only with stereo analog inputs. A good way to compare it to the Model 990 would be to use a DVD with a stereo track (Dolby 2.0) and apply Pro Logic IIx to that. If you want, you can then use PLIIx-Music and player with the Pro Logic II settings to see what you think. Also, system calibration could be a sticking point. Based on a link I found, there was apparently an HK clone of the Fosgate Model 4, and I found a manual for the HK. It included some test tones for calibrating each channel, but I have no way of knowing what differences may exist between the two systems' test tones - they should be comparable, but I don't know that for certain and there are still possible inconsistencies between the two. Did you use the 990's auto setup, or did you calibrate manually with an SPL meter?