Haven't had any problems with the new software...back before the update I had this glitch where Enter Sandman would sync a new copy every time I connected my Zune. I reformatted and that fixed it, by the time I did that I had 300 something copies though
I will say that I believe a lot of my previous problems with album art/weird stuff happening was because I was trying to use the Zune software to tag, which is a nightmare. Now that I'm using MM + Mp3Tag to tag, my music syncs to my Zune fine.