I have two databases:
master_
testsite_
..with separate users master_master and master_slave assigned to each database (master_, testsite_ respectively).
The master Joomla site is installed on the master DB, the testsite replicated to the testsite_ DB.
When I install a 'novel' template (ie not installed on any master or slave site), it is installed in the /templates folder of the master site with the database table entries in the testsite's DB. Is this how you've made JMS to work?
In some scenarios, having the template installed in the master site's template folder would not be an issue. It is an issue for me, though. I need the template to exist in the testsite's template folder so I can modify the css, etc. Furthermore, installing the current WARP patch/plugin shreds everything. At one point, I was getting symlinks to templates in the /administrator folder of the master site. When that thing fails to patch perfectly, it destroys the integrity of many settings/files on a multisite. The ZOO patch is at the root of the problem. FYI, I'm using the latest version of ZOO (..20).
Here's a snapshot of the settings, you should be able to replicate the conditions from this: