Thanks again.
Yes all the records are set-up correctly - before I started using MFT I hand coded all my Gedcoms, which is why it's so frustrating - I can see perfectly good code in a text editor, and each separate gedcom loads perfectly but merging them creates havoc - I guess I'll need to do a manual merge and see what results I get.
(I googled GEDCOMit and didn't turn up any (useful) links to software - do you know who makes it?)
Thanks again!