People who like to use some of the more advanced LaTeX features sometimes run into problems when trying to put things on the arxiv. The arxiv uses a relatively old LaTeX distribution (TeX Live 2011) – which is a big upgrade from TeX Live 2009. If they continue the update pattern, they will adopt the latest TeX Live distro every other year.
Hence, if you just install the latest TeX Live on your Mac or Linux machine, some packages cause trouble. One example is the biblatex + biber combo which is a replacement for bibtex. Two reasons made me switch away from bibtex: bibtex is not good at handling non-ASCII characters such as umlaute (ä, ü, ö) and accents (e. g. é and à). The second and more important reason is that it is hard to customize the output of bibtex to your liking. As the arxiv does not run bibtex or biber on the server, the bibliography needs to be created on the client computer.
Biblatex and biber have seen a major upgrade from TeX Live 2011 (v1.7) to TeX Live 2012 (v2.6), and it turns out that the output is mutually incompatible. On the other hand, biber had had some trouble handling large bibliography files on OS X, something that has been fixed in the latest release. Even though I have tried to include all necessary files, in the end, I gave up and switched back to TeX Live 2011 on my machine just to process this file using the old version of biblatex and biber so that the output is compatible with the arxiv. Fortunately OS X allows you to easily switch between the different TeX Live distros in the System Prefs. I have also had to shorten my bibliography, but fortunately that is something that can be automated using BibTool, for instance.
So if you have trouble submitting things to the arxiv, install TeX live 2011 on your computer and switch to that once you are ready to submit to the arxiv. Then submit.