I know this is an old post but this is relevant for anyone else like me setting this up and going into a Klingon battle frenzy thinking this is true:
found out from amd tech that the drivers are not made to use 2 cards without xfire and they are not planning on adding that functionality because the demand isnt there... yet nvidia does...
Just got my other second hand freebie Radeon today and was having this same problem also. Read this part and just about had an aneurysm. I have been having freezing problems with my single card setup and was desperately hoping this would fix it without spending more money which I don't have anyway.
KKKKKHHHHHHAAAAAAANNNNNNN!!!!!!!
Turns out this is all wrong (its worse than that, he's dead Jim) - and thank Shatner (hallowed be thy name) for that! It may have been true at the time but is now illogical Jim.

The trick I found was that you have to recreate your window layouts from scratch.
My guess:
The Display handles are hard coded into the ISboxer configuration and cannot be changed from the GUI on an existing layout. For example my original monitors were identified as "Display 1" and "Display 2". Now they are "Display 8" and "Display 10" or some rubbish.
Of course when the window binding happens it is hard coded to bind to display 2 which no longer exists. (verified this in the innerspace console.) Then through some GPU Dx Magic it displays on the secondary monitor but is GPU'd on the primary graphics card.
Recreating the windows layout has solved this and even though you do not see any visual difference the GPU meters do not lie.

Also the console is now "forcing Display 8" as it should.
This
will effect people who change up their monitor setup (e.g. adding/swapping/removing) and triggering a relabeling of key monitors. (I have now tested it) So something to be aware of.
I imagine you can edit the xml directly yourself also and I saw the handles in there to do so. It seemed relatively straightforward but I wanted to be sure so recreated.
Not sure if this is a feature, fix or bug that needs to be added to the backlog or not? But there is a workaround.
Anyways. There you go. There is hope for broke people like me with crappy video cards.
This setup works amazingly well and no freezes or crashes yet so I Sulu level happy with this. Also the cost of this setup (even had I bought both cards new) was fractions of what I would have spent on a single card.
PS: I am not really a big star trek fan - just a crazy person.