Changing Blog URL loses theme settings

I have read the official wordpress release on moving sites and have done this many many times. When we move a site to a new domain (usually from http://www.site.com to www-dev.site.com or vice versa) we are finding that some of the theme and or plugin settings are not copying over.

I do a full search and replace on the database dump and then reload it into the new database file, so I would imagine this should be an exhaustive replacement of all the url references. There are no references to the site URL in the theme code.

I’m not really sure of the wordpress internals here — maybe the settings are hashed against the old site URL and that’s why they no longer work with the new URL and the sql search and replace doesn’t matter. Anyone else experience this or know what the issue is?