I think some of the issue might be that every time I tested MP3's, I had no cover art. My old mp3 library was very random with lots of bit rates and hardly if any cover art. My flac library is completely flac, excluding podcasts, and it all has cover art. I'm thinking the cover art generation slows it down a great deal. If I spend many hours creating cover art on my main computer and move to my theater computer, all the cover art has to be regenerated and it seems to unlink the cover art from my main computer. The cover art seems to slow it down quite a bit if I have an image turned on for each song.
It also could be Vista. I think Vista seems a bit slow but I need to reformat again and see how it runs from a fresh install. The install I did copied my old system files and installed on free space...meaning everything probably got fragmented and really messed up.
Also, is there a command line option to resize cover art when music is being converted? I store huge cover art files and syncing with cover art copies this jpg to every mp3 which can really add up at 1 MB per song. I may just disable cover art completely until we can find a solution since it really takes a huge amount of space at 20-30%.