When you click the button on the taskbar for an inactive window to make that window active in Windows Vista or in Windows Server 2008, the currently active window is selected again
Consider the following scenario. You have an application that has several owned WS_EX_APPWINDOW pop-up windows. Then, a user selects an inactive window in this application from the taskbar of a computer that is running Windows Server 2008 or Windows Vista. In this scenario, the currently active pop-up window is selected again.
For example, assume that an application has a main window and the owned pop-up windows C, D, and E. Pop-up window D is active. You click the button on the taskbar for pop-up window C or E to make that window active. Instead, pop-up window D remains the active window.
For more information on this issue, including potential causes, workarounds, and resolutions, see: Microsoft KB Article KB955562.