After about half an hour, with no solution being provided, I did notice that when using the bigpond webmail site (normally use a pop3 client), that a lot of the missing messages had been put in the webmail Junk Mail folder.
It would appear that anything that comes from zoneedit is automatically labelled as junk.
The fix might be as simple as adding an exception for whatever bigpond thinks is the junk trigger. Pretty hard to do it for every domain/address I have, so I guess I'll manually check the junk folder via the web interface and see what other legit emails end up in there.
Hope this info was useful to someone.