MBP Retina, Mid2012 2.7GHz Intel Corei7; 16GB OSX10.8.4
I'm working to finish a statistical analysis project using a large dataset and an SAS program called JMP. I'm using an old version of the program (8.0.2) which I cannot update because of expense. (I will eventually receive new stat software from my new employer, but need to finish this project first.) JMP occasionally hangs on high processor loads with rolling beachball and unresponsive windows. I save my work a lot, and am muddling through, but there's a weird variation on the usual behavior that I haven't seen before. Once it hangs, I can kill JMP from the Terminal or Activity Monitor, but JMP's open windows stay on the screen. JMP is truly dead-- it disappears from the menubar and it's gone from Activity Monitor. It doesn't seem to spawn any daughter processes (at least none that are evident in the heirarchical view in Activity Monitor). I can restart it, but the new instance doesn't seem to recoqnize the old windows, which persist alongside new windows. They can be dragged around, but can't be minimized or closed. Mousing over them gives me the beachball. Everything else seems to behave normally. The only way to get rid of the windows, though, is to reboot, which I can do normally.
My question, entirely in the interest of speeding my workflow, is how do I kill these zombie windows short of reboot? I tried restarting the Finder with no effect. "sudo kill -9 windowserver" just reboots. Is there anything short of that?
For extra credit, one additional weird symptom is that Top (run in Terminal) doesn't display results when JMP is hung in this way. I can run it, it seems to be active, but it doesn't display any text. Activity Monitor and Menu-> Force Quit display active programs/processes correctly.