There are various ways to get into the situation where multiple explorer.exe's end up running on a single-user Windows 7 system. (explorer shortcut, renamed executable, etc.). This can result in multiple explorer.exe tasks running. When this happens and a user alert from the agent needs to be displayed, then a duplicate user alert is displayed.

This issue is under consideration to be resolved in a future release.

As a workaround, avoid having multiple instances of explorer.exe running on Windows is required.

When the checkbox for Select the Launch folder windows in a separate process  is enabled, explorer.exe launches every time Explorer starts.
If the checkbox is enabled, disabling it can prevent multiple Desktop Alerts from launching.

How to verify the settings for  folder option on Windows Vista or Windows 7

 1. Start Explorer and strike the Alt key on the keyboard.
 2. In the upper right hand side of the page, click | Tools | Folder Option | View | to display Advanced file and folder settings
 3. Verify if the checkbox for Select the Launch folder windows in a separate process  is enabled or not.  If it is enabled, disable it.

How to verify the settings for  folder option on Windows 8 or Windows 8.1

 1. Start Explorer and click | View | Option | View | to display Advanced file and folder settings
 2. Verify if the checkbox for Select the Launch folder windows in a separate process  is enabled or not.  If it is enabled, disable it.

If Explorer.exe launches everytime when Explorer starts although the checkbox for Select the Launch folder windows in a separate process  is disabled, there is possibility that Windows could have another reason to cause this issue.