System does not recognize second monitor

I am using the fglrx 14.1 driver for my GPU. when I plug in a second monitor KDE does not recognize it, however Catalyst Control Center and xrandr can find the extra monitor. I can configure CCC to extend my desktop across both displays, but KDE is still convinced there is only one display. When I open an appkication the bouncing icon of that program appears on both monitors but the cursor does not, also I can’t add a default panel to the second monitor. I am sure this used to work 2 weeks ago, I did a full zypper update to make sure I was using the latest software, but the problem did not go away. I remember doing a BIOS update, but I can not recall if this was before or after these problems started to appear.
I also found a second problem with my display, this started around the same time but I am not sure if it is related to the above. When i put my cursor in the upper left corner, I should see all open applications, however I can see the green thing showing up but not all open windows, now it gets even weirder when Catalyst Control Center is opened the screen edge does work but when it is closed again it stops working. Is the above cause by some (BIOS) update or is this one of the many bugs in fglrx.

I tried uninstalling fglrx and then KDE does recognize my second screen, so it is fglrx related. Somehow fglrx prevents KDE from seeing monitors.

I did some more experimenting, and discovered that turning xinerama on solves all the issues. I am puzzled on how it did work before with xinerama off. Sadly turning xinerama on causes more problems than it solves, is there an alternative that does not break desktop effects, sound and internet?

I found a workaround, I configured the Catalyst Control Center to think the 2 displays are 2 parts of 1 big display, this solves the problems above, however on reboot these changes are lost and the displays start in cloned mode, how do I make these changes applied on boot?

For future readers this is what I did:
-open catalyst control center.
-go to display manager
-select the multi-display tab
-select Multi-Display desktop with display(s) 2.

These settings will be lost on reboot.