Did this just happen? Or has it always been this way? If it just happened, you need to think about what changes you made to your software and or drivers that caused this. If this happened after a driver update, you may want to rollback to the last driver you remember CrossFire working for you. Do a complete uninstall and use something like Driver Sweeper or Treexy Driver Fusion to clear the remnants of the old installations away.
If it happened after you installed a program (maybe game related or not) that runs at system start up or something that's running in the background before you start you games, try disabling it before starting you game. In the past some running tasks have been known to interfere with CrossFire.
Do you have CCC running on your System Tray? If not you may want to try it with it on, or vica versa if it is running.
The CAP mismatch shouldn't be causing your problem, however if you run out of things to try, I wouldn't count it out.
It seems to me that your system isn't detecting 3D applications and therefore isn't enabling CrossFire when they're started.