Comment 2 for bug 777417

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.