I am having the same problem and tracked it down to the rotation. If you change the rotation on the second monitor from "left" to "normal", I am pretty sure everything will work. Here is a temporary workaround --
1) Set all rotations to "normal" in xorg.conf, but have everything else set the way you want it.
2) Start X.
3) Go into ATI Catalyst, and change rotation of desired monitor. Settings will be applied immediately, and everything appears to work (unless you were to now restart the X server at this point -- DON'T!).
4) Go back and edit xorg.conf so that rotations are again set to "normal". This won't affect the current session, but will allow you to reboot without hanging.
You'll have to repeat steps 3-4 every time you boot up...