I used to have that when I used Presets to move between Eyefinity and Extended - I generally had to select the profile twice in order to get the screens set up the right way.
I now simply use Disable Eyefinity Group or Re-enable Eyefinity Group in CCC, and my screens always end up the right way round (once I'd set them up first time, obviously) with just the one click.
If you're using all your screens in your Eyefinity Group, you could try using Windows+P to switch between profiles. Press Windows+P, select Extended and set up your screens as separate monitors. Then press Windows+P, select Duplicate and set up your Eyefinity Group. You should now be able to use Windows+P to easily move between Eyefinity (Duplicate) and separate monitors (Extended).
I would suggest having a play and trying all three methods to find the one that works the quickest/best way for you. I've used all three over the past few years depending on my setup at the time.