I managed to find the problem references by converting the referencing to the Diabetics style, which numbers all references and then seeing which numbers just had a full stop next to them, finding those numbers in the text body and cross-referencing to another copy of the document that was unformatted to see which references were at those locations. NB when formatted the references appear in the text as a blank spaces.
I found that one was a missing government department field from a government document (this one doesn’t have the problem until I delete the other completely unrelated one – I’ve tested this several times!), the other was an imported journal reference from a webpage that had incorrectly been set as a book chapter by the page that I’d exported the reference from, there was no book editor and hence no listing in the bibliography.
After switching it from book chapter to journal I still couldn’t get them to appear correctly in my document even when using update my reference from library (it was showing correctly as a journal article in the box that appears). So, having read how to force the travelling library to be replaced I tried saving the document as a new one with the citations unformatted and then closed it. I then reopened it and updated citations and they still appeared as a full stops!
I tried that again having removed the original references from both the document and EndNote web-deleted and then permanently deleted (unformatted and reformatted the document to check the full stops had gone), created a new citation online and reinserted the citations in the document, they still appear as a full stops!
Strangely if I add another reference first and then add the problem one it appears as it should…but only until I delete the extra one, then it reverts to the same problem! If I insert the problem references somewhere else in the document at random they suddenly work, until I remove the unwanted ones and then they revert to being full stops.
I’ve tried saving the document with a new name with unformatted references and then opening it on a completely different computer that I’ve never had the endnote plug in on previously, this was to make sure that the travelling library is completely removed and recreated, and the problem still happens.
Deleting both of these problem references from my document creates a third, I haven’t dared try to delete that one to see what happens.
The references work fine in a new document, but starting over isn’t an option for a 50 page chapter of my thesis – if I have to do that I will change referencing software at the same time.