I had the same problem.
Here's the fix:
You've been messing with your admin/includes/configure.php. I changed mine to have a local test setup and my shipping and delivery modules disappeared.
The problem was, I cleared this definition as such:
define('DIR_FS_CATALOG', '');
when in fact it needs to be set to an absolute path like this:
define('DIR_FS_CATALOG', 'C:\Development\TestWebsite/');
and when I run live on the webserver:
define('DIR_FS_CATALOG', '/home/public_html/');
Good luck.