As a workaround, the correct icon can be copied from 
/usr/share/icons/ubuntu-mono-dark/apps/
and converted to png with:
for i in *.svg; do rsvg -w 24 -h 24 $i ${i%%.*}. done

I got so annoyed by the yellow icon, I couldn't wait for the correct fix
:-)

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Icon for tomboy in notification area is different from icon for tomboy applet
https://bugs.launchpad.net/bugs/552292
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