Patching removes file security settings

[BSOD2600]

I've noticed that when I patch files, as directed on the patch website, the new patched files lack most security settings.

For example, I installed the script_server_file_header.patch. I executed it in the root of my Cacti folder and it patched lib/ping.php. Getting properties on the file, one can see it is inheriting the security from the root of my cacti directory.

Any idea why the heck this happens?