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It is standard behavior on Windows for applications to post multiple formats in the clipboard buffer when copying. Often they only post an "IOU" reserving the actual data movement for some future time when an application requests the data in response to a Paste command.
Calibre quite properly follows this behavior and posts a variety of formats. You can view the options by accessing the Windows accessory app "Clipboard Viewer". The "cure" for the OP's issue is to use the Windows standard "Paste Special..." option in the app used for Pasting. Not all apps have this, but all good ones do (and my browser of choice, Opera, fails at this -- bad Opera). The OP can check this with his copy of Notepad++ which provides the option (though the menu option is oddly located far below the "Paste" option). Using an intermediate app to "Paste Special..." the desired format and then re-Copying is a reasonable workaround that will usually work.
It's true that many apps fail to support "Paste Special...". We had issues with this back when I was on the FreeHand team at Macromedia. Too many of our users needed to paste into other apps that failed to support Paste Special and we added a rather unique "Copy Special" options that allows manual control of the copy format on a per Copy basis.
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