The problem appears to be due to the way that bold characters are handled. A quick example using R2014b:
plot(0:0.01:2*pi,sin(0:0.01:2*pi)); xlabel('\eta'); print('-dpdf','test')
The above code creates the correct pdf using the default export settings. When the font is changed to bold however, the "eta" is printed as "2"
Changing to a raster image format (eg png) does export the text correctly, but I agree with Aaron. Raster graphics are not good enough for publication.