File Manager does not save permissions of file/folders. Just click on desired permissions, click save and then you will still get empty permissions.
File Manager uses the following type of command to set permissions:
cmd.exe /c runas_silent.exe -w -u w001234567 -p xxxxxxxx --command "icacls.exe "\\servername\share-name\webspaces\webspace_id//wwwroot/testfolder" /grant:r hosting\i00xxxxxxx:(OI)(CI)(R)"
However when the webspace default ftp user (for example w001234567) has % or ! in the password it is replaced by white space which results in command failure.
Internal issue with id POA-92607 'Webfilemanager fails to fetch or update permission when webspace ftp password has %' has been submitted.
Please contact your TAM or PTA team in order to clarify the status of this issue. As a workaround, please change FTP user password to the one without %.