The sixth episode of the first series was a Christmas special, so that might explain that. And it says 30 minutes on the show page, but the episodes all run about 25 minutes, which I believe was the correct broadcast length. (EDIT: just checked my mp3 of S1E2 against the Sounds version, and they both run exactly 24:16.)
My understanding was that the episodes on the series one CDs were as broadcast, but the ones on the series two CDs were the edits that the Beeb made after the fact for later rebroadcasts (somewhere around 2 minutes shorter) and that they junked the originals, meaning the only versions of the full-length s2 shows available for a long time had the edited portions reinstated using notably lower-quality sources. Of course, I now have much better sounding cassettes of the original s2 broadcasts that I got hold of via eBay a couple years back that I'd be willing to copy and digitize once I have access again to the proper equipment, but nobody seems to be interested in that...