I am using Matlab to make a data plot for one of my thesis figures. I use inkscape to annotate the figure and add graphics. I export the figure as .eps and import with inkscape. What's strange is that I set the font size of the axis labels to 10pt using Matlab, but inkscape imports it as 12.5pt. What's even weirder is that after annotating the figure, exporting to .eps, and compiling the figure in a latex document, the font size is back to being 10pt. Anybody know what's going on?

The answer lies somewhere between the 72 and 90 dpi working models perhaps?
12,5/10=90/72.
Inkscape works with 90 dpi, while other programs usually with 72.
Though the font size is changed, the size of the text object is the exact same.

Yes, that has to be it. When setting my axis titles to 8pt font in Matlab, inkscape imports the .eps as 10pt.
10/8 = 12.5/10 = 90/72 = 1.25

But, that leads me to believe if I create a drawing from scratch using inkscape, the fonts will all be off by 25% when I export them and print? That can't be right, can it?

*EDIT: Ok, after further review, the answer is yes, I will have to multiply my inkscape font size by 1.25 to get the actual output font size correct. Further reading here: viewtopic.php?f=29&t=5530

For printing it is always safer to convert texts to paths, and save as a pdf.

I asked the same question on #inkscape @ irc.freenode.net and they pointed out, that the default unit for displaying fonts in Inkscape is px. So when you in MATLAB specify fontsize 12, then it is by default 12pt. When you open that in Inkscape and see "15" displayed in the font size input field, then it is 15px, not 15pt. You can hover your mouse over the font size input field and it will display you the unit.

Also pointed out by people in that IRC channel: Inkscape is no postscript processing application, so when you open an eps in Inkscape it has been converted to PDF and then to SVG.