Search the Squeezebox forum under the Audiophile section. There is talk about installing some plug-ins/software optimizing the server to improve streaming quality. I haven't tried them myself yet, but from reading the postings it supposedly does make a difference.
One setting on Logitech Server software that I did make which I found on SoundCheck's blog is the setting the decoding file type for FLAC
AIFF - Disabled
FLAC - Disabled
PCM - FLAC
Doing this will have the server decode (unpack) the FLAC file so the SBT doesn't have to do the work. I recommend checking out SoundCheck's blog also for more recommendations.