Went through the rules and I can't seem to see anything that answers what the difference between the two jammed guns damage cards are...other than a few are red and a few are green. What is this newbie obviously missing?

The answer is found on page 18 of the Burning Drachens rulebook (English version), under Scenario Rules.

Bullet Checker

"Bullet checker" pilots checked every single bullet before taking off and discarded the defective ones, so when they fire, ignore the jamming damage result on cards with a green cross; bullt-checker pilots jam only when their target draws a card with the red cross.

A similar rule is in the "On the way to become an ace" scenario, in the Famous Aces / Watch your back! rulebook.

You can also check the FAQ here:

http://new.fantasyflightgames.com/edge_minisite_sec.asp?eidm=24&esem=4

Have fun!

Andrea