I have seen this with Bob and Joey, even after a year. It does not usually last, and then they are friends again.
I think you are doing all the right things, and keep doing what you are. I think that it is probabaly what other have suggested. Maybe an alpha cat syndrome or it could also be really rough playing.
Let us know what happens.
Good luck. Just continue to be a good mommy to your babies and you will work though this.:)