Is your Source Distribution folder different than the Server Root folder? You can check that in the QMC, System, Setup, QlikView Servers and Distribution Services. Check for either .QVW, .Shared and .Meta files.
Is that happening to all the reduction and distribution tasks or only for this one? What version of QlikView are you running? Did you upgrade or did a fresh installation?
I've ended up in the very same situation. All tasks in the publisher ends up in duplicated entries in the accesspoint.
Just upgraded to QV11 and rearranged the folders to look like below.
The server folders are these:
Mounted folder 1:
The distribution source folders:
Because you have the "Documents" folder in both the Root and Mounted folder, all sub-directories will be inventoried in AccessPoint. If you require the control that Mounted Folders provide, then ensure that they are not on the same branch as the root or other mounted folders.
In your case, creating an empty folder "C:\ProgramData\QlikTech\Documents\root" and setting this as the Root folder in the QEMC should solve the duplication.