A verbose log would give you clues. When Windows Installer processes the 
RemoveFolders action, if the folders aren't (yet) empty they will be left 
behind. If the completion of the file removal was delayed beyond the end of the 
RemoveFiles action it is usually logged in verbose installer logs.
 
One frequent reason is virus scanning systems.
 
> From: christoffe...@flowcentric.com
> To: wix-users@lists.sourceforge.net
> Date: Wed, 17 Jul 2013 10:35:16 +0000
> Subject: [WiX-users] Folders not removed on Windows Server 2012
> 
> Hi, When I uninstall a web site using my created MSI on Windows Server 2012 
> not all folders that where created by the installer does not get removed on 
> uninstall, the folders are empty but still there.
> 
> When installing/uninstalling the same MSI in a Windows 8 machine all the 
> files and folders that get created does get removed as expected.
> 
> Both machines has AUC enabled and the installers does get elevated.
> 
> I do have the correct RemoveFolder elements in the components.
> 
> I'm just not sure why it will work on one machine and not the next.
> 
> Please can anyone advise on how this is possible?
> 
> Thanks in advance.
> Christoffel
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