Well I had everything on my desktop set up satisfactorily, then my 2 year old got a hold of the keyboard...

I had it set up so that inactive windows were translucent. However, the toddler attack has now made it so that if there are two instances of a program running, if one has focus the other goes opaque as well. Even if it's underneath other windows that are translucent. I'm assuming it's some sort of application grouping, but I can't figure out how to change it back...

I would recommend checking your Window Rules in System Settings.

The only rule I have is "(Default) Disable focus stealing prevention for XV"