A formatting note for your post: you managed to wrap your code in code tags, but not the directory listing; the preview should have shown you that. The latter part of your post should like this:

These are the permissions on the original directories:

ls -ld /usr
drwxr-xr-x 54  root sys  69 Apr  9 2018 /usr 
ls -ld /usr/include
drwxr-xr-x 117 root bin 436 Sep 25 22:10 /usr/include
ls -ld /usr/include/sys
drwxr-xr-x 25  root bin 628 Sep 25 22:09 /usr/include/sys
[download]

When I extract the archive(as root) generated from my code I see these permissions:

ls -ld usr
drwxr-xr-x 3 root root   512 Jan 20 13:06 usr
ls -ld usr/include
drwxr-xr-x 3 root root   512 Jan 20 13:06 usr/include
ls -ld usr/include/sys
drwxr-xr-x 2 root root 11776 Jan 20 13:07 usr/include/sys
[download]

Thank you for any assistance!

Do you see how this makes your question clearer?