Suppose that you are debugging a web application. Browser with the application is open in the XFCE workspace 1, Eclipse is open in the workspace 2.
When breakpoint occurrence happens (and you are in the workspace 1), Eclipse appears in windows list. You click it and Eclipse is now open in workspace 1 (the same where browser resides).
In GNOME this works as supposed: when breakpoint occurrence happens and you click on the Eclipse in the windows list, workspace is changed and Eclipse is open in its initial workspace 2. Workspace 1 is left with browser only.
P.S. Linux Mint 13 Maya XFCE.
This sounds like something with xfwm4, not xfdesktop related. Moving bug report.
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