Thanks gonk. I have not experienced any audible differences, except with some extremely high dynamic range recordings (e.g. Telarc's recording of Olympic Fanfare) where I notice a very subtle loss of "punch" in the FLAC recording. I just wanted to make sure that it wasn't due to any difference in the 990's settings.
I did some A/B comparisons between my Media Server via USB and the original CDs via optical connection, and this was the only recording where I could tell the source, but only when doing immediate back-and-forth comparisons while both sources played simultaneously. I suspect this is an issue with either the server, the settings I used for extracting/encoding the song, or limitations of the FLAC format. My next experiment will be to copy the CDs as an ISO image and play the image from disk as a virtual CD-ROM drive. That should take the extraction/encoding method out of the equation.
I have not seen many reviews about the 990's capabilities via its USB connection other than from those who see it as a convenience feature. I tell you, this is proving to be a real gem.