When you export a figure to .eps in MATLAB, it will only use a small number of allowed fonts, even if the user has changed these fonts to something specific to their system. In most cases, you'll end up with 'Helvetica' specified in the resulting eps file. That is, if you import this file into Illustrator and have no font exactly called 'Helvetica' then you will end up substituting something else for it, often times doing bizarre things to your kerning, etc. like moving your subscripts to Siberia.
This script writes the .eps as usual, but figures out what font you actually used in the figure and does a find and replace to place your font (presumably actually resident on your system) back into the file. Currently this does not discriminate between the axis font and other text fonts in the figure (i.e., the title and added text), so everything gets changed to the axis font.
This is just a workaround until Mathworks decides their .eps exporting is problematic.