OK. I seem to have solved it. Although I am not quite sure how and given the seemingly random nature of the problem it may not work for everyone. But I hope it does.
I tried pretty much everything, from restoring and installing new firmware and completely uninstalling and reinstalling MM. Nothing worked.
However at one point MM picked up my iPod as an external drive and while it let me sync I couldn’t access anything. So I removed both devices (proper iPod config. and ext hard drive) from my options list and reconfigured my iPod properly. I synced and the tracks played perfectly.
So I went in to the options to see what may have been causing the problem. Turns out that at some point since Sunday (last day of known proper plays) I must have ticked ‘Copy Album Art to Track Tags’. I tried to sync with this option ticked and the tracks started cutting out again. I unticked it and they were fine. I have no recollection of ticking it but I guess like many new MM users I was playing around with different settings.
This explanation also makes sense of the fact that some tracks cut out earlier than others. My music collection has been through several music manager programs, from Creative Mediasource to iTunes, to WMP and back to iTunes again. Many tracks have therefore accumulated a lot of superfluous album art. The track (Big Time by Peter Gabriel) that was cutting out with 2/3 seconds left was had one piece of artwork attached and one cutting out with 13 seconds left (The Future by Leonard Cohen) had… erm… four. Don’t know how that happened.
I’m going to try incrementally resyncing my playlists and playing random files to see how they are holding up.
Finally, one minor point. ‘The Future’ is displayed on MM with a time of 3.47 but on the iPod as 3.46. So it still cuts out slightly sooner than it does on MM. To be honest this is only noticeable on this track as it is from a soundtrack and there is dialogue at the end. ‘Big Time’ is displayed as exactly the same length on each. So I presume this is something to do with how the iPod handles certain VBR files. As I said, not really an issue. I seem to remember similar things happening on other players.
So there you have it. Try unticking Copy Album Art to Track Tags and it should hopefully solve the problem. If you do not have it ticked I’m kind of at a loss. But it does seem to come down to how the iPod is configured in MM.