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This works as you suggest.  I have actually managed to get
this problem with 2.1.1 as well now.  I think that the
problem is with GTK when a g_message or g_warning is issued,
it causes the console to open.  The console doesn't actually
appear right away, only when it gets to the g_message or
g_warning.  Any output that would have appeared before that
is missing, but any output after it does appear ( I think). 

I'm using pygtk0.6.6 to write a GTK-based python app, but
there's lots of C code too.

I will look in glib and see if I can find out what it might
be trying to do ... the unfortunate side effect of this is
that I doubt I can get you a short example unless you are
set up with pygtk.  I could provide binaries though ...