Greetings thegallery,
You may be thinking of NVIDIA's nView Desktop Manager, which disappeared a while ago, and is now back. If one of your controllers is an NVIDIA controller, try looking in the Classic View of Vista's Control Panel and look for a separate nView Desktop Manager icon. If it's not there, make sure you have the latest driver.
Once you open it, make sure nView Desktop Manager is enabled, and you should see a lot of tabs detailing different settings. Transparency is under the "Effects" tab. It is also available in the upper-left title bar icon menu under each application once nView Desktop Manager is running.
nView can interfere with a number of applications when all of its default settings are tunrned on, so turn off everything you're not using, particularly the title bar buttons in the "User Interface" section.
And you will of course need to reload the XP driver and lose Aero Glass itself to get both controllers working simultaneously. But if the functionality of the transparency feature is more important to you than the Aero Glass animation effects, this is a small price.