Yes, the running order was different. There were seven runs of episodes, plus 'Bells' which aired as a Christmas special in 1984 (two days before the US got to see it, fact fans!). There's a mostly-complete list of episodes here:
http://muppet.wikia.com/wiki/Fraggle_Rock_(UK)
Fulton Mackay appeared in all 48 shows of the first two US seasons with the exception of 'Manny's Land of Carpets' which eventually aired with Simon O'Brien in 1989, plus 'Bells'.
After Mackay's death, John Gordon-Sinclair played 'P.K.' for 24 episodes from 1988-89 and Simon O'Brien played 'B.J.' for the final 24 from 1989-90.
It isn't clear how many of the 96 shows produced still survive, although there are certainly far more than the 12 that were released on DVD a few years ago.