Tony, I just upgraded to 2.0b3 and am seeing very similar results to what you described. Further, while doing a shuffle of my top-level, I seem to be getting only tracks from one of the sub-playlists (my "download" list).
This absolutely was not happening when I was running 1.03. Not even close. I may get two tracks by Bob Marley within 20 tracks, but they'd probably be from two different discs. And I doubt they have any code to check for such things (read my post about shuffle in the wish list).
Ugh, this is pretty nasty. I didn't used to use any type of random when listening to CDs, mainly because I thought it was useless changing discs through the magazine in the car or carousel at home. With the immediate nature of spinning tunes off a hard drive, I think it's a feature I'll use quite often (yeah, yeah Archeon... You don't realise how useful something is until you start to play with it :)
Another strange thing about updating to 2.0... I had exactly 5859 songs being listed on the empeg with 1.03 - the EXACT number of tunes I actually have. For some reason there's now a mystery digit floating around, so it reads 5860. Weird.
Bruno