This may be a problem with java applications in general.
Problem began at some point after a restart, subsequent restarts have not fixed it, nor has uninstalling/reinstalling java (openJDK-7) and the minecraft launcher itself.
When I try to run it (from the console, using java -jar launcher.jar) the normal text pops up in the console, but the window for the launcher does not appear. An icon for it pops up on the left side of the screen, and if I hold alt and hit tab, it will show up in the list of available programs. Right clicking on it while holding alt will show what the launcher should look like, and clicking on it will cause the active window to lose focus, but will not bring the launcher into focus. The launcher is absent from the Master+W screen, and attempting to resize/maximize the window from alt-space causes Unity to seize up for a moment before returning to normal function.
Anyone have a clue what's going on?