I believe this issue is on OS X only, as I could not reproduce it on Linux:
Using tikzexternalize, the pdf is not updated whenever I change the tex-file. Instead, I always get the following answer (from latexmk/pdflatex):
===== Image './figures/main-figure0' is up-to-date. ======
Even if I manually delete the pdf, the figure is not rebuilt. It does not even check for the source file once the final pdf is ready. I suppose this has something to do with time stamping on OS X, but have no real clue how to get this working.
Any thoughts/suggestions/debugging possibilities?