Please attach the corresponding dmesg output.

Does this still happen with xf86-video-ati 7.9.0?

(In reply to OmegaPhil from comment #0)
> I found that when I turned it off for ~10 seconds or more, after turning it
> back on all screens would go black and appear to reinialise. XFCE4 gets
> confused and clones the primary monitor output to the new 3rd screen,
> fiddling in the XFCE4 Display program fixes this (after the problem happens
> it seems to put the primary and new monitor on top of each other...).

FWIW, this could be an XFCE issue, unless xrandr reports incorrect information
about the connected monitors after this happens. Xorg only informs clients when
something might have changed about the connected monitors, it doesn't perform
any configuration changes by itself.