I have the SAME problem on my 60 gig player. I have a 12 gig player that has no pauses between tracks at all. My 60 gig player sometimes changes tracks instantly and sometimes takes 2-3 seconds to go to the next track. I also noticed that when I fast forward to the next song, sometimes it is seamless and sometimes it hangs for a second or two...
I just chalked it up to 60 gigs instead of 12 gigs = more time to wait. Who knows, maybe the 12 gig drive I have in my EMPEG is better then the two 30 gig drives that are in my Rio. I guess that means EMPEG really is better then RIO!!!