Okay, I have to admit...I've never tried to compare two Greek texts. I thought I could just open the Text Comparison panel and view them side-by-side like my English versions. This doesn't seem to be working though. I mean 98.5% difference between two "majority texts"! lol 
It appears that since they use different Greek fonts (accented) the comparison is getting all messed up.

What am I doing wrong? Is there a better way to do this?