I had this exact same thing happen a bunch of times about a week ago. Currently I run an SLI setup with dedicated PhysX my issue was I upgraded video drivers and forgot to set the dedicated PhysX. I know the game does not use PhysX, but it correct this issue for me.
The game needs better support for Xfire/Multi-GPU builds.
I have 3x R9 280x in Xfire across 5760x1080 eyefinity setup.
I get like 60 FPS on one card and like 61fps on all three lol
Horrible support for Xfire/ATI