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calibre registers with default programs, telling it what filetypes it is capable of opening. It does not register itself as the default handler for any filetype.
The user (or some program she runs) has to change the default file types for that to happen, calibre itself does not do that.
In your case I'd guess you have something messed up in your system. Either the registry is corrupted or you have a third party tool interfering with file associations. In either case, doing a simple system restore should revert the changes.
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