I'm a fan of using Windows in a "focus follows mouse" mode. That is, keyboard input is directed to the window the mouse is in, even if the window hasn't been "raised" to the top. This allows me to keep matlab plots in the foreground while typing into the command window in the background. There are various registry edits or programs like TXMouse that enforce this kind of behavior in Windows.
However, with my recent upgrade to Matlab 2014a (from 2011b), Matlab appears to enforce a autoraise on focus on all of their windows. (This happens only with Matlab windows including figures and the command window.) Any thoughts on how to control the raise/focus behavior in Matlab or otherwise return to my preferred mode of operation?