I believe this is your problem. You accidentally use DialogueTrigger2 three times :)
<img src="http://s22.postimg.org/enot5monl/Support0035.png" border="0" />
Will the collisions still work even though the bullets and enemies are on different layers?
Yes, collisions are across all layers.
I must admit, you have a nice piece of work here. Very well put together. Good use of Groups and comments. There are some obvious bugs here and there, as well as some redundant code. But, over-all, great work so far.