How do I turn focus follows mouse off?
I have a feeling that you likely resolved your issue since this was a few months ago, but just in case someone else runs across this in the future:

I had this exact issue - no changes to use preferences and this just happened all the sudden. It wound up being a special system extension (an awesome one, minus this Focus follows mouse feature) called Afloat. It has a menu bar option in all OS X applications under Window>Focus Follows mouse that is easily accidentally selected.