ianh,
I do something similar. I use a linksys music bridge and router to send all audio from my computer to the 990. The music bridge has a digital optical out that I feed the 990 with. I have used a variety of lossless codecs using various software (iTunes, MusicMatch, etc) and none have been as good as the original CD. Currently I use dbPowerAmp to rip my CDs in FLAC format. dbPowerAmp also allows conversion of most formats to any other format. For example, I convert the FLAC to mp3 for my iPod.
My latest listening tests have been at the same volume between FLAC files played on dbPowerAmp to the 990 via the linksys and the original CDs. I have used the 990 DACs in both cases and the original CDs sound better. Fuller, as you described, better mids and highs and the bass via the music bridge is also a little boomy. I can partially compensate for the difference by using the softwares 16-band equalizer, but I've not been able to force the two to sound the same. I don't have an explanation why 1s and 0s sound different via the computer/linksys setup versus the original CD, they just do. I do believe the weak link is the router/music bridge. I suppose if I had the ability to run some cat5 between my computer and HT gear the sound might be better. I don't think it is the FLAC files since I have compared CDs burned from FLAC files with original CDs and found them to sound the same.
I use the linksys equipment and dbPowerAmp when I'm not focused on just music. It provides a convenient way to have some background music and the dbPowerAmp software does a fine job ripping CDs for my archive and for making CDs for use in my cars.
If someone has a suggestion on how to improve the sound via the computer to the 990, I'd gladly give it a try.
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AvFan
Outlaw 976 | ATI 2005 | M&K 850s Left, Center & Right, Surround-55s, MX-70B Sub | Harmony 950 remote | Panamax 5100 | OPPO UDP-203 | LG OLED55B7