When a php page is working on the root of the domain but not in any sub directories, the permissions are wrong. Any directories that need to run php need to be set to 755.

While trying to install Mambo CMS the installation page would never come up errors with 404. The CPanel Apache Error log shows – SoftException in Application.cpp:238 “..file.php” is writeable by group. The log file points to a problem with the file but it is actually the directory. The php file should be 644. Installing Mambo from the tar/zip file the default folder permissions needs to be set. This is similar to an inherit permissions. In Linux this is set with the cmd ‘umask’. To have all new directories created with the 755 permission set as default, ‘umask 0022′. Now when a new directory is created from mkdir or new extracting an archive, all directories will have 755 permissions.