Using the 7.1 Direct input and the 990, the 990's DAC's still come into play unless you have all speakers set to "LARGE" (signal is converted to digital for bass management and then back to analog) - I doubt it's related simply to differences between the Sony's DAC's and the 990's DAC's.
When you are using the optical input, you may be applying some surround processing - doing so can have a huge impact. This is most likely what is creating the disappointing sound. The mode that I use mainly for CD's is Upsample (use the "STEREO" button and press it repeatedly until the 990's front panel says "Upsample"), but you might also try Pro Logic IIx-Music (press the "DOLBY" button repeatedly to get it), NEO:6-Music (press the "DTS" button repeatedly), or 5 Stereo (or 7 Stereo depending on how many speakers are configured, accessible using the "STEREO" button) to see what you think of the most common music modes.