I just downloaded the latest version of the program (very nice, BTW) to check out some potential gear changes on my Combat Medic. Worked great.
However, I noticed something odd. After entering all my stats in and having it calculate stuff, I decided to compare the bonus healing, crit chance, etc info the program gives against the in-game character sheet. Everything matched up except one: Bonus Damage. From what I can tell, the program's Bonus Damage number isn't taking into account the bonus from Cunning.
Minor thing, but I thought you'd want to know.