In the Hype's interview with Kevin Feige, he said that both Fox and Marvel were able to use the characters, but Marvel couldn't make reference to mutants or Magneto.
SHH: What about the future of "The Avengers?" I don't know if you want to bring in new characters or just keep the core team. Characters like the Scarlet Witch and Quicksilver, are they part of Fox's deal or are they characters you could use?
Feige: We both have them. There's a specific arrangement with those two characters that would allow us to use them with "Avengers," but not discuss or reference their mutant or Magneto-related lineage. They can use them as mutants and as Magneto's relatives, but cannot have anything to do with "The Avengers."
SHH: So whichever universe uses them first basically gets to keep them.
Feige: Yeah. Contracts are always complicated. (chuckles)
The last bit is significant about whichever one uses them first gets to keep them. Now that may not be necessarily legally, but in the public eye, that would be the version of them first established. So maybe it's a rush to get Scarlet Witch and Quicksilver onto the big screen first so that the Marvel version will be the true version and anything Fox puts out will be seen as a pale imitation.