Woohoo! Got it working
I found that the disk integrity check was running every time, so fixed that with FSCK. Synching was then happy, but the web playlists still didn't work. I figured it was still a problem with the root playlist, so deleted it using jEmplode (emplode won't let you do this). A sync on jEmplode made it all very messy, so I didn't save it. Instead a sync with emplode rebuilt the root playlist (and renamed it from playlists to allmusic :/).
Don't know what the problem was or how I caused it, but all is now good.

Rob