I've had a closer look at my Y axis (with its .05mm of click) and in the spirit of finishing a story - it turns out that the problem lies with the FK12 ball-screw support bearings, which are rumbling a fair bit. Not great news, but a lot less hassle / expense to put right than replacing the screw and nut...

As for my musings on the Z - well, I posted a while back that I wasn't entirely satisfied that the screw was straight - but once it was installed and working without any noticeable issues I was happy to leave it at that. In retrospect (and ignoring my erroneous 'theories' above) it's very likely that the run-out in the screw is what contributed to it seizing. There, the penny dropped. It took a while...

New FK12's on order, will attempt to recondition the old as a spare set.

Wal.