I found the post below a couple weeks ago and decided to change my default Greek font to a BibleWorks font so that my Professor using BW could read the greek text in papers I submit.
http://community.logos.com/forums/p/21633/162241.aspx#162241
It came as something of a surprise to me this morning while working in my Interlinear Septuagint that I was unable to read the english in-line text. With a little effort I was able to figure out that the english text was still in English (sort of), just transliterated using greek font with the English words. When I went back into the program settings and reverted to Gentium I suddenly could read my interlinear again!
I know this isn't terribly important, but it would be kinda nice if at some point this was fixed so that those of us who want to use alternate fonts can do so and still have our Interlinear Septuagint.
This problem does not seem to impact any of my NT Greek Interlinears.
-Tim