Take MediaWiki, it is GPL licensed (not AGPL), so you can modify it and run an instance of it without sharing your changes. Except, when someone accesses it, you are redistributing MediaWiki's GPL-licensed JavaScript files to their browser, so you do have to share your changes[0]. Think how many sites there are violating that without even realising.
Now think how you configure MediaWiki; you modify LocalSettings.php to (at the bare minimum) add the database username/password, and set the secret key.
This means essentially every site running a MediaWiki installation (or Wordpress, or effectively any other GPL-licensed web application) is violating the GPL, and are only getting away with it because no one has bothered to take legal action over it.
That is not a problem with MediaWiki, but that copyright on JavaScript has not been acknowledged or enforced since it was created. Site like archive.org, spiders, and scrapers are regularly copying JS, and most JS libraries I have seen lacks any copyright information whatsoever. Many media sites gives out JS snippets for users to include (for inline video, images and so on), but do not add a license permission to include (copy) the JS.
You modify LocalSettings.php which creates a derivation of MediaWiki, or as the GPL puts it, "thus forming a work based on the Program". At this point you don't have to share the changes.
However, once you distribute the JavaScript files:
"You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License [...] These requirements apply to the modified work as a whole."
By modifying LocalSettings.php you have created a derivation. By redistributing the JavaScript files you have distributed part of the work and therefore must make the whole derived work available under the GPL.
Take MediaWiki, it is GPL licensed (not AGPL), so you can modify it and run an instance of it without sharing your changes. Except, when someone accesses it, you are redistributing MediaWiki's GPL-licensed JavaScript files to their browser, so you do have to share your changes[0]. Think how many sites there are violating that without even realising.
Now think how you configure MediaWiki; you modify LocalSettings.php to (at the bare minimum) add the database username/password, and set the secret key.
This means essentially every site running a MediaWiki installation (or Wordpress, or effectively any other GPL-licensed web application) is violating the GPL, and are only getting away with it because no one has bothered to take legal action over it.
[0] http://lwn.net/Articles/609709/ (section: "JavaScript and the GPL")