Just started running dual cards as well, now I'm seeing issues.
While runing with a single 560ti and dual monitors, windowsfx5, and deskscapes 3.5 all was fine.
Wanted to offload the 2nd monitor to another weaker video card (7950GT) and ADD a 3rd monitor.
So now my layout looks like this:
Primary card - 560ti with samsung 27" LED
Secondary card - 7950GT with Gateway FPD1775W and HPS2031.
Not SLI'd (not possible, not wanted)
Upon reboot Aero would crash once the desktop was loaded. Then as I opened a few windows, the computer would become unresponsive. Tried multiple reboots with the same result.
Trying to track down the issue, I eventually disabled windowsfx5 in msconfig, and now the computer works just fine with new video card / monitor configuration, including Deskscapes 3.5. It is truly amazing that I have 3 different anamations for each of the 3 monitors. WOW 
I would like to get WindowsFX5 working again, any suggestions on what to try ?
I did notice one thing that seemed odd:
Nvidia control panel reports the configuration CORRECTLY, however Deskcapes reports the monitors INCORRECTLY as:
Your computer has a Windows Experience Index base score of 7.2
Your Windows Graphics Experience score is 7.8
DeskScapes appears to be activated on this PC
DeskScapes engine appears to be running
(SyncMaster P2770H/P2770FH (Digital)) 1 is attached to NVIDIA GeForce GTX 560 Ti
() 2 is attached to NVIDIA GeForce GTX 560 Ti
(Generic PnP Monitor) 3 is attached to NVIDIA GeForce 7950 GT
Deskscape.dll 2011/11/01 13:10:18
Deskscapes.dll 2010/09/27 09:06:03
DreamControl32.dll 2009/11/09 15:10:17
DeskscapesConfig.exe 2011/11/01 13:10:45
UI\Deskscape.dll 2011/10/26 11:13:21
UI\DeskscapesVideo.dll 2009/10/24 11:04:54
DreamTasks.exe 2010/09/24 12:01:26
DeskscapesVideo.dll 2010/01/19 16:02:22
Willing to help with any suggestions you would like to have me try.