popup windows are not controlled by the window manager." Of course, that means you have to position the window manually, which helps work around your other gripe, that you didn't like the position so much. ;-)
Well ! Here is a complete example to display popup tooltips on the hotspots in a image. (Also includes the image to go with it) Enjoy it / patch it as you feel like. Regards, Ofey.
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popup.tar.gz
Description: GNU Zip compressed data