I have an 80GB and am having some of the same problems mentioned in this thread: freezing when I try to play a different song when there is 15 seconds or less of the current song left and then having to reboot, time counter doesn't progress on some songs. On songs in which the timer does progress, it sometimes begins late, stops, or shows the wrong time. In addition: occassionally after the end of a song, the "now playing" screen does not switch to the screen for the next song (but I can hear the next song), sometimes pressing the right side of the zune pad makes the player advance to the next song, but the next song does not begin playing unless I press "play", and "pause" does not work most of the time. There's just so many things wrong with my player that I probably haven't even mentioned everything. I've tried the two fixes mentioned (returning the background back to the default and re-installing the games); neither worked.
I just got my player this August, and like with most of you here, none of these problems existed until immediately after I installed the 3.0 software. I've never dropped it or had any problems prior. I'm debating what to do next, but I hope Microsoft offers some type of fix soon. I just switched over to Microsoft after I dropped my Creative Vision M in water a few months ago (had it for 2 years with no problems), and I LOVED my Zune prior to this update. It's extremely frustrating.