Did someone already encountered this problem with ATI cards?
Sorry to say: yes.
same setup, with 9800XT or so cards. dualhead span mode 1400x1050@50Hz was impossible to set up. Three grown men, brave and skilled technicians, close to tears after two days of fiddling around. Buying NVidia Cards saved us last minute.
Conclusion: Do not use ATI cards if you need control over
a) funny resolutions (say: dualhead 1920x1080),
b) frame rates (like the esoteric 50Hz, oh my God)
c) Dualhead setups.
As it stands, NVidia drivers (while they have their shortcomings, too) are far better configurable. There is also an API and some Pro users have begun to write their own safe-start C++ helper apps to override the control panel settings.
However, having said that, did you try powerstrip, and / or the latest omega drivers?