Mmm, I tried copying part of it into a new document but referencing worked perfectly! Am reluctant to put entire thesis up as an example. Maybe I should just recopy the whole thing into a new document. Will try that!

Someone showed me how to delete hidden metadata and that has helped to a certain degree. I think it's just such a big document 120,000 words with lots of tables and figures and no doubt mega-deletions etc that somewhere along the line the referencing system has given up the ghost!

Thanks