My 60gig Mk2a also sometimes "waits" 2-3 secs before starting to play the track. This only happens when I've skipped a (or more) track(s). I figured this was still a bug in b11, since this didn't happen in 1.03.
I guess it will be resolved in a future upgrade. Apart from some small problems (like this one), I've been very happy with b11 so far.