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I didn't realise it was the citations in the captions that was causing the issues, since the figures appeared after each specific reference had been cited in the body text. I only discovered it when I did as you suggested and remove figures from the files.

I've managed to fix the problem. I was using the \cite{...} command in captions for figures and tables. Since LaTeX runs the toc builder before it runs BibDesk, this meant that the \cite{...} commands within captions were read before they were read from the main body text.

To overcome this, I used ...

I think it must be an error with how BibDesk has copied the citations across (can't think how though, because as you say it should be the same). When I made the "test" file, I renamed the citation references in BibDesk and manually in the .tex files, in order to make it easier to show which order ...

I did exactly as you requested in the above post, creating a duplicate document without any of the words in it, just cite commands, and I couldn't replicate the problem - the references were all in the correct order.

Could this be caused by using the "Copy cite command" option from Bibdesk, and ...

Unfortunately the document cannot be made public at this stage so I cannot post the files in their entirety. I have tried creating an example file using exactly the same formatting, code and files as I have, but this does not reproduce the problem.

The main page for the LaTeX is given below. I ...

Hi,

I'm using BibDesk with LaTeX/TeXShop and am having some problems with the "unsrt" bibliography style. Basically the bibliography (\cite{blah}) entries are not being numbered in the correct order.

For example, the first instance of \cite{...} in the .tex file is numbered as reference [2], the ...