I may be confused, but if you have your HTPC connected to the 990 via SPDIF, isn't the 990 doing all of the digital conversion ? The 990 will decode DTS and DD but I don't believe it will go beyond that.That may be why your having a problem with " advanced resolution". When playing dvd-a or SACD, I always do the digital conversion at the source and pass the signal to the 990 via the 7.1 analog inputs ( though with 2 channel recordings, any analog audio input would do ).
I hope this helps.
I do mostly classical music on SACD, but I find the high resolution audio to be far more involving than redbook CDs or DD DVDs.
That being said, when there's a DTS option available on the disc, I generally use a digital connection and do the decoding on the 990.
Enjoy!