So I updated to El Capitan and I reconfigured the Latex paths from /usr/bin/ to the /Library/Tex/ etc. and my document compiles fine, with no error messages in the screen output, EXCEPT certain .eps figures just simply do not show up in the document.
changing the order of the Figures and it seems the first two figures (whichever I specify) are the only ones that show (so it's not an issue with the figures/.eps files themselves)
compiling a .tex file, which worked and showed all figures before the El Capitan update and sure enough, only about 2-3 figures showed compared to the 20 or so that are meant to show.
changing the sizes of the figures, whether they go across both columns or just one and that has no effect.
pdflatex instead of latex, dvipdfm and the output is the same.
Anyone ideas what's going on?