Mavericks window loses focus on Cmd+Tab
I can't help with this but I can confirm that this is one of many issues with multi screen multi window applications on mavericks. As he says, when you have 2 windows of the same app open on different screen, it will always give focus to the one on the primary monitor when you cmd+tab away and back to the app. This makes it rather annoying for development work when you are switching between a browser and editor regularly.