I took a quick look and I see a small issue. In "Left_Motivated_Behavior_Final.ino" line 199 you are asking if the fed3.Right is triggered and then calling logLeftPoke() instead of logRight Poke(). I think if you fix that it will work.
Please post back if that fixes it!
To explain what's going on: when you poke Left or Right it sets a variable fed3.Left or fed3.Right to be true, respectively. The FED3 code then does things based on that variable being true, and when it finishes logging data it sets fed3.Left or fed3.Right back to false, completing the poke. In your case, when you poke on the right it will set fed3.Right to be true, but then your code calls fed3.logLeftPoke, which will increment the left count but then set fed3.Left (and not fed3.Right) back to false. So when the code goes around again it will keep acting like the Right poke has been triggered, and calling fed3.logLeftPoke (which increments the LeftCount). Anyway hope this fixes it! -Lex