I searched the Mendeley support forum and found out that I was not alone having a problem with the automatic installation of the Microsoft Word plug-in from the Tools menu. The solution that worked for me was a slight modification of one of the Mendeley agent’s suggested solutions:
Install MS Word plugin from the Tools menu in Mendeley Desktop.
Browse to C:\Users[YourUserProfile]\AppData\Roaming\Microsoft\Word\Startup
(The path might be slightly different on your machine. Remember also that the AppData folder is hidden. To make this folder visible, click Organize in the window toolbar -> Folder and search options -> View tab -> Hidden files and folders -> Show hidden files, folders, and drives)
Copy the file Mendeley-1.7.1.dotm
(Alternatively, you may also find this file in the C:\Program Files (x86)\Mendeley Desktop\wordPlugin folder)
Browse to C:\Users[YourUserProfile]\AppData\Roaming\Microsoft\Word\Autostart
Paste the file in the root of the folder.
Done!
The solution was to put the global template Mendeley-1.7.1.dotm
in the Autostart folder instead of the Startup folder, which seems to be the normal folder for global templates from what I have read.