I was surprised to find this little Zolnixi of mine who has visible Spirit Flames when both her parents have visible Butterfly Wings.

http://www.sylestia.com/view/pets/?petid=123715
(Sorry, on an iPad, will post an image later)

Her grandad on her mother's side had visible Spirit Flames, so she probably got it from him.
And looking through linages, she also has a great-grandma on her father's side that has visible Spirit Flames, so it completes the puzzle.
Really interesting to find that out. c:

from what I understand, the order the genes are in in the list is the order for most dominate to least and also that there is something about being able to see if a pet carries a gene for another trait (Someone posted once how to figure it out but I can't remember)

So I would assume that has a lot to do with it.... just like real life genetics

Yeah, there is an order of dominance. What happened is that the father and mother were still both carriers of Spirit Flames but since Butterfly Wings are dominant that's what showed on them. The offspring has a chance of either inheriting a Spirit Flames gene or Butterfly Wings from either parent. If she had inherited Spirit Flames from one and Butterfly Wings from the other she would have had Butterfly Wings as well. But in this case you had an offspring that inherited only Spirit Flames from each.