Vendor wanting me to exclude folders

Hi, we run HP Worksite (formerly Interwoven) on our network. Since the install of Webroot, I have had a few people mysteriously lose documents that they were working on during the day.
 
They save and close the doc, as per usual. But when they check it, none of the changes are checked back into worksite.
 
Their support says we need to exclude the following folders and subfolders:
 
%temp%NetRight
%appdata%InterwovenNRPortbl
%appdata%InterwovenNREcho
C:NRPortbl
C:NREcho
 
Ive found out that webroot cant exclude folders, only files. However these folders hold all the temp docx files that a user creates when they check a document out of worksite. So there can be hundreds of files that open and close inside these folders, and there is no way of explicitly knowing the filenames etc etc.
 
As for trying to say it isnt webroot, the vendor support immediately identified the cause of the problem as AV, and I didnt even tell them we had changed AV software.
 
Im not too sure if anyone else uses worksite and webroot, but how do I go about meeting the requriements of the software?
 
Thanks,
Nathan