The main problem here is that a pygame window doesn't set any window
atom value for "_NET_WM_PID", so for libwnck it's impossible to find the
PID related to the opened window, and so the launched command that would
make BAMF associate the application with the proper .desktop file.

So I think that this is not a BAMF problem at all, but you need to set
this value to make your application being recognized properly or
(better) to fix pygame to make it set more informations related to a new
window that it creates.

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https://bugs.launchpad.net/bugs/777417

Title:
  Unity launcher doesn't work well with Python Pygame apps

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