I wanted to provide an update with more details of my problem. In Matlab R2014a and earlier, the figure I want to make looks like:
I plotted this using standard plot commands and exported as an EPS file using the "print -depsc filename.eps" command. I have done this for over a decade in many versions of Matlab. It always works the same. The uploaded figure is generated after opening in Adobe Illustrator CS6 and exporting as a PNG since EPS files can't be displayed online easily.
Now, if I run the exact same script in the new release, Matlab R2014b, the figure looks the same in Matlab, but the exported EPS file looks like:
Most critically, the fonts no longer pass through. I had Helvetica plus a symbol font before. Now, despite the fonts showing up fine in Matlab, the fonts in the EPS figure are all screwed up. Illustrator gives an error when opening the file that says it cannot find the fonts "any:" and "any-Bold:". This has to be something to do with the new graphics component of Matlab R2014b, but I don't know what code to use to get around this since the code that has worked for a decade no longer works. I'm not doing anything weird.
I should also not that the print command takes a lot longer to run. Bracketing the command with tic and toc gives 0.25 seconds in R2014a but 3.08 second in R2014b. Something is really messed up with R2014b but I am hoping there is some sort of work around. For now I will keep using Ro2014a but welcome any suggestions.