A cursory glance and read up suggests that ATI Tray Tools does not specifically offer the same customizibility that CCC offers with regards to Eyefinity..
If you're planning to upgrade to new hardware and adding new windows, a fresh new installation of the 64bit version of your Windows would be best, it would offer you a clean slate, and have a higher probability that these issues will not arise..
Being a card carrying ATI/AMD user for quite the past 8 years or so, I've dealt with many issues related to ATI/AMD graphics cards and their drivers/driver support for games in the past; one of which had the exact same symptoms like your problem, which is why we did the whole song and dance with those utilities yesterday.
As a heads up, you can use the key that came with your 32bit version of Windows 7 for the 64bit version as well if it is a retail version; just deactivate your 32bit version prior to the upgrade via Microsoft Support and activate your 64 bit version of 7 afterwards..
Thanks for being patient and cooperating with me yesterday...