I have some plots created with TikZ and pgfplots. In the captions, I use \ref{...} with plot labels in order to get the marker printed there; a neat feature indeed.
Now, when submitting to arXiv one has to jump some hoops in order to make the document compile with their horribly outdated TeX Live (2011 at the time of this writing). In particular, I use TikZ externalization because TikZ has evolved a lot, and uplading the figure PDFs along with the LaTeX sources nicely circumvents problems.
The problem now is that said references to pgfplots plots resp. their labels fail to resolve; I get (??) instead of the marker. Needless to say the problem does not occur locally.
Is this something I can circumvent (short of hard-coding the marker there for arXiv), or do I have to live with it (i.e. hard-code the marker instead of using the reference mechanism)?
I don't give an MWE since I don't consider a fake submission to arXiv reasonable.