I faced the same issue in all versions of matlab. I always get a different font in the exported eps file.
So here is one method i use each time.
Save a MATLAB fig file with the formatting you want for different elements e.g labels etc. Export eps/pdf from this and verify if it is ok for you.
Now the simple trick is to execute your program without plotting figures.
1) Import the above mentioned saved fig file in to matlab and open plot editor. 2) Delete its variables from plot brower 3) Import your variables which you want to plot (click on figure and then click add data tab in plot brower) 4) update label and title (text only, no font changes) 5) Save file as .fig and also export to eps.
You are done and you get the same formatting in each figure you generate like this.
It is a time consuming process but gets your job done. Also in case you want the formatting of a fig file saved with other version of MATLAB this method works, even if OS is changed or fonts are upgraded.