This is a strange one, that seemed to start after I upgraded to VDT 2.51. I'm running Windows XP Professional, and use Auto-Arrange to keep my desktop icons in order. At my screen resolution, I can place 10 icons in a column, and I have over twice that many. For some reason, the XP desktop is now only making one column of icons. The result is that all icons after the first 10 are off the bottom of the screen, and inaccessible.
It's interesting to watch as my computer boots. The icons initially are placed correctly, until VDT starts up. As soon as the virtual screen is set up, the icons switch into one column. It's as if Windows thinks I have much greater desktop area than I really do.
I use a virtual screen with four virtual desktops, in case that's relevant information.
Using 2.51, you can use different icon positions in virtual desktops. However, Auto-Arrange must be disabled when using the workspace manager; when Auto-Arrange is enabled, the workspace manager should disable itself, but it seems that I missed something I will correct this in the next release (probably on next week).
Before this new release is available, you can disable the workspace manager. First disable the Explorer's Auto-Arrange feature. Right-click the VDT icon in the notification area, go to "Settings" and then "Virtual Desktop Toolbox"; go to the first tab, and uncheck the "Enable the workspace manager" option. Then you can re-enable the Explorer's Auto-Arrange feature. Unfortunately, you must finally log off and on again as the "Workspace manager" is a startup option.