I have two separate x displays running kde. So right now this browswer is in focus, and when I alt-tab, the second display is the one that switches windows. Out of the 3 times I just pressed alt-tab, two were on the second X and one was on the first X screen.

Is there an option so that alt-tabbing is done relative to which X has a window focused?

Using KDE 4.9

Multi-Head is basically unmaintained in the KDE Workspaces. In this case the problem is the global shortcut system which is not multi-head aware and sends the command not to the correct KWin instance. My last testing with Multi-Head showed that this is a general problem for all shortcuts.

My recommendation: think about whether you really need a Multi-Head setup and consider switching to a normal multi-screen setup.