So this question steams from an experience I had and have been pondering sense.

I was making a cake for my BF who loves lemon (the more sour the better). I made a batch of Indydeb's butter cream and put in a product called Brauns Dessert Lemon Paste instead of a wilton flavoring.

Now, I have never had any problems coloring the butter cream recipe I use but when I mixed in a WHOLE jar of wilton black coloring it turned the frosting green ... So I guess my question is why? What exactly is in clear flavoring?

Maybe I am not wording this wrong, but I don't understand why the color didn't take and I figure the only think that I changed was the flavoring. In the future, if I want something other then Butter, almond or vanilla flavored crusting icing, what can I use that wont affect my coloring?

The acid in lemons can badly effect colouring, and I'll bet that that's what turned your icing green! You will need to use an artificial flavoring for lemon if you don't want to take the chance of it altering colours.

Wilton only does the three right? I have seen the candy flavorings and I wasn't sure if I could use those in BC or not....

Yes you can, Loran oils too, just go sparingly as they are super concentrated!