In some apps that I run as administrator in Vista, scrolling with the touchpad only works in one direction (depending on the app). Scrolling with an external mouse works just fine. When not run as admin, touchpad scrolling also works just fine.
Apps that I've confirmed the problem with: MS Visual Studio 2005 (Team Edition), XEmacs
System: Vista x64 Home Premium, Synaptics touchpad (most recent drivers installed for my notebook, v10.1.8)
It is quite possible that your touchpad drivers save their settings per user, so that when you run anything as the administrator account it will load that account's copy of your mouse settings.
If you've got an app or a Control Panel applet that you can use to configure your touchpad try doing a Run as Administrator on that and checking the settings to see if they're the same as you expect.
I experienced the same problems with latest generic Synaptics drivers (version 14.0.3).
The problem imho is not caused by the driver, but it's the SynTPEnh.exe, which is responsible for the scrolling and other features (kill the process in TaskManager, and two finger scrolling won't work an more in any application).
If you manage to run this tool with elevated privileges, two finger scrolling should work even for applications that were started as administrator.
One way to do this is to create a task in the task scheduler, that will start SynTPEnh.exe with highest privileges at logon.
Is this a ThinkPad? If it is, are you using the drivers that Lenovo/IBM provides or are you using the generic Microsoft drivers?
