Thanks all for your suggestions. After playing around this morning with the moon, I think I've finally discovered the problem, which is, in retrospect, trivial, but may be of use to others.
The cap for the polar scope was on tight, and the RA setting circle appears not to be well seated, so when I had the setting circle tighened against the RA axis it was causing just enough friction to cause juddering when tracking slowly, but not so much that things didn't appear smooth at any faster speed. The RA circle appears to be slightly out of true, which is why it was worse in some orientations than others, but not consistent.
When I loosened off the RA circle, the problem disappeared, although it means I can't use the RA circle for manual setting, but that's a relatively minor problem!
Hopefully the fix will be confirmed when I give the scope a good test tonight. Otherwise, I'll be back!
Phew....