I think what started a lot of this mess is that a while back, Autumn Games and Konami were sued over a Def Jam Rapstar loan. This caused problems for Skullgirls, as it was also co-published by Autumn Games and Konami, and due to the lawsuit I think a lot of money was tied up and couldn't be used to continue to pay the Skullgirls crew, who wanted to continue working on the game. So they cut ties and reformed, changing from Reverge Labs to Lab Zero, and did a Kickstarter to fund their continued support of the game, and moved to new publishers.
It seems like this separation and reforming hasn't gone quite as smoothly as it could, and Konami is making it harder than it needs to be for whatever reasons.
I don't know if my info is 100% accurate as this is all from memory, but I think its the basic gist.