First thing I'd do is actually bring up the install/install.php scripts. Some servers, depending on what they are running and the configuration, don't actually need the permission changes.

So I'd bring that up and see if it's giving you FAILS. If it is then you'll need to set the permissions, but since they aren't actually changing you might not need it.

Another thing to consider is if you are the owner of the file.
On your ftp program check the owner/group number on the ones you can't change permissions.
If you have some files you can change compare the owner/group number
You may need to call your host to allow you to change the permissions.

just coming to this forum post has helped me out a lot!
appreciate it guys. Talk soon
John