We have a server running cPanel 10.9.0-RELEASE 9808... when the user uploads a file (say test.cgi with permissions 755) through the File Manager and checks the "Overwrite existing files" box, the permissions for the script revert to 644... anyone have any idea how I should approach this?
If the upload is happening via the web browser, HTTP has no concept of filesystem permissions, thus those are not retained by the file upload. Use FTP instead.