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When uploading new files and directories to the server, via SFTP logged in as a normal cpanel user, on a brand-new server 'CENTOS 6.8 x86_64 standard WHM 58.0 (build 23)' it seems that default permissions are wrong. The original files/dirs are all 644/755. When I upload with my GUI client (Transmit on Mac) the directories are being made group writeable but the files are ok (644/775), causing problems with suphp of course. Anecdotally, I believe I have a client using WS-FTP Pro on Windows...

SFTP - Incorrect upload permissions