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Python GTK can use several clipboards, but Windows only uses the CLIPBOARD one. Need to figure out how to enforce the use of the correct one.
Correction, this is actually an old problem cropping up again: http://seclists.org/nmap-dev/2012/q1/592
I somehow got the pygtk package downgraded on the Windows build system, reintroducing this bug. Next release will be fixed.