Here's how I've solved the problem!
In the Catalyst Control Center app, which you can open by right-clicking a blank portion of your desktop and clicking Catalyst Control Center in the context menu, click on the Gaming button on the left. Then click 3D Application Settings. This window will appear:
Scroll down until you see the AMD CrossFireX for 3D Applications heading, and click the pull-down box:
Not surprisingly, the default mode is called Default Mode. For me, the mode AFR Friendly worked for Prototype 2, so click that mode:
Scroll up to where it says <
Once you've saved, you may discard the custom settings in CCC, and then close it. Launch Prototype 2, and see if it works for you as well as it worked for me!