I can't seem to reproduce the issue anymore. The program in question was utorrent v2.x.x, currently I am running v3. I don't know what caused it and what I exactly did to resolve it.

salival wrote:On the second desktop I set in the desktop configuration panel to execute the program at Dexpot startup.

Which program? Do the icons return if you click the "Show Desktop" button?

The rule was as follows:

On the second desktop I set in the desktop configuration panel to execute the program at Dexpot startup. (Configure Desktop>Desktop 2> start tab)

This will have as a result that the program will execute and be on Desktop 2, but there are no icons on desktop 1 when you right click on the desktop you will not get the context menu.
When you close Dexpot and restart it the program will be on the 2nd desktop all will be as expected.

This is on Windows 7 x64 by the way with two virtual desktops.

When you let windows execute the file and then set a rule to move the window to the second desktop in the desktop rules panel you will not have this behaviour. This is what I use now.

salival wrote:I have set a rule to start a specific program and move it to a specific desktop when Dexpot starts.

What's the rule exactly?

I have set a rule to start a specific program and move it to a specific desktop when Dexpot starts. Dexpot itself is set to load when windows starts.

The issue I'm having is that when windows starts Dexpot opens the program and moves it to the 2nd desktop as it should. In the process, however, desktop 1 has now become empty (no icons) and the right-click menu of that desktop doesn't appear.

After I shut down and restart Dexpot all is restored to how it is supposed to be: icons only on the 1st desktop and the program on the second.

When I shut both the program and Dexpot down and restart Dexpot it works as expected and there are no issues.