Windowed mode after killing zsnes
That might work, but to be honest I am done messing around with this, at least for now. I got it to work almost the way I wanted to. The thing that really should be done here in the long run is that xbmcbuntu should come with openbox pre installed and setup so that xbmc runs inside openbox window manager as default. That way you could run any program you like straight from xbmc, no scripting needed.
I know this thread is a few months old, but try going to Advanced Launcher, go to your zsnes launcher, edit launcher, advanced modifications, and change "Toggle XBMC into Windowed Mode". That worked for me when I was having a similar problem with snetflix.

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