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bbfa235
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(Get the code!)
It appears that the issue is caused by a color depth issue.
For me, when running gnome-do from the console I get:
"Gdk-WARNING **: Attempt to draw a drawable with depth 24 to a drawable with depth 32"
Using xwininfo, I can verify that the preferences dialog is the only window on my desktop thats running in depth of 24 (even the dock is running in depth 32).