I know this is an older thread, but I don't see how John solved the issue. Can anyone provide suggestions? I'm experiencing a similar issue on my server.
Moodle version 2013051406
Moodle release 2.5.6 (Build 20140512)
Server: Windows 2008R2 Server, IIS 7.5. DB: SQL Server 2008
Like John originally mentions, I suspect the problem may be cache related. The database has the proper values, but the code seems to pull the settings from the cache. Adding some PHP "echo" statements to the page show that the cache is returning the original values, and hence populating the page improperly. We're only using the basic cache settings on this server. I've attempted purging "all caches" a few times.
Other plugins seem to be respecting their setting changes.
Thanks,
Peter