We cloned our live site (moodle 2.9) to make a development installation, cloning the database resulted in the live & development sites having the same "siteidentifier".
This had the consequence that both installations were now sharing cache (the siteidentifier is used to identify which cache to use, see document section on sharing cache). So if you changed the theme on development, it changed the theme on the live site and vice versa.
The solution was to delete the siteidentifier on the development site, moodle automatically creates a new siteidentifier, then all was good (I wrote about it here Cloning Moodle).