It would be good to see if going back to the current build "breaks" it again (which tells us it wasn't just something messed up with your original install of build 96). Also... Other applications (things set to run automatically) can sometimes steal focus, so make sure you don't have anything running (even hidden) that might be launching new processes or other things like that on a periodic basis. I've seen it with scripts I've written, photo processing, backup and sync tools, video transcoding applications, and other similar things.
The best bet, for testing, is to make sure the computer isn't doing other background tasks of any kind (kill everything in the tray, pause all tasks in Task Scheduler that you may have created, etc), and try to reproduce. If it doesn't happen then, slowly add stuff back one at a time till you find the culprit.
I haven't seen any focus issues with Theater View with current builds, for the record.