As I said, I've had this problem for several days now. I've narrowed it down to only happening when ISBoxer is running my SWTOR chars. When I have my two windows open, everything else I try to open (Chrome, Evernote, whatever) exhibits this flashing behavior. Switching between SWTOR windows with my hotkey makes them flash, etc. Clicking on the flashing tab won't switch me to the flashing window - I have to use Win-Tab to cycle between open windows to actually change windows.

I am not sure why, but the problem does seem to be ISBoxer.