First, the QVS service needs to be restarted. Secondly, you are probably looking in the QVS folder which is C:\ProgramData\QlikTech\QlikViewServer\ . Have a look instead at the Document Root folder, which is by default C:\ProgramData\QlikTech\Documents\ . The PGO files exists as a copy in both files, but the XML files are only being generated in the latter one.
If the change-date of the PGO files are not recent, you have probably changed your Document Root folder to somewhere else, check QMC > System > Setup > QVS Settings > Folders > Root Folder, and see what the path is set to.