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I've only encountered something like this on one or two occasions.
I think you've hit the nail on the head around your registry. There might be remnants there from before that makes it think you have the update already. I am guessing it looks elsewhere beforehand to decide you need the update, but then gets confused later on.
Try removing/uninstalling what you can of the app then use a registry cleaner to remove anything related to it that remains in the registry. The cleaner I use will want to remove anything it decides is redundant when it isn't able to find files for an application associated with it.
Once and awhile I've seen update download problems if I don't exit from my pop-up killer and/or firewall.
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