OK - fixed it, after a dive into the templates (50multi-drop) to see how it works.
The multi-pop entries in /etc/fetchmail are not updated unless the e-mail retrieval method is being set to 'multi-drop' from some other type. This, in engineering talk, is an 'edge triggered' event.
To ensure multi-pop is turned on, switch the e-mail retrieval method to 'standard', save, then back to 'multi-drop'. This bounces the multi-pop functionality into action!
It may be possible to get away with pressing 'save' on the e-mail retrieval screen without changing the method from multi-drop. I didn't try that (in fact - I just tried it and it works. You must hit "save" on this screen if you make any configuration changes to multi-pop).
Ta,
Jason