If you could help with the bug submission once you are satisfied that would be great, thank you.
Excellent - thank you. What is the next step?
(Incidentally, and not surprisingly, I have discovered that any paragraph set to outline level 1 will have the same effect as the first heading 1)
What is important is not Heading 1 paragraph style but the outline level. The TOC engine (and other “chapter” features) are not linked to a particular paragraph style but to the outline level defined in the style. This allows many interesting efects by using several level-1 styles (such as numbering chapters with standard and Roman numbers in the same document). But this is not the present bug.
Next step is bug report. I’ll file it and mention the link in my answer. You can then check its correctness (reading the bugs doesn’t require credentials.
Thanks - seen the bug (and the duplicate warning) and that looks fine. I notice that under “version” in the bug report it asks for “earliest release” … I can confirm that the same problem exists in OpenOffice 4.1.6, so I guess it is long-standing (from before the fork, anyway).
Thanks for all your help with this … now to find a workaround! … 
Andrew
Workaround: it all depends on what you do with your journal. Do you need continuous page numbering across articles? Do you print it or display it only on scree? Are there any cross-references between articles? Do you need all articles simultaneously?
It is going to be printed … and I think I have found a workaround (courtesy of a colleague). As it happens, left-hand pages have a fixed header anyway, it is only the right-hand pages that are affected. Only two articles have enough endnotes to cause the problem, and as a result only two pages are actually wrong. What I have done is to add a borderless frame to each of those pages, anchored to the page and covering the header, and typed what I want into the frame … :-).
Fine. Otherwise, you could also print the whole master document but for the faulty articles. The faulty articles would be printed from their respective slave documents, taking special attention to the page numbers.
Yes, I did wonder about doing it that way. I need to create a single pdf to send to the publisher, so was considering exporting it in pieces, as you say, and then stitching them together with PDFSAM (have you come across this magic tool?). However, I think it is easier to export the whole document to a single odt and then play with frames … it is then one simple export to pdf.
Thanks again for your help and support - we will wait and see if they get round to fixing the basic problem … :-)!