One question is if the books are from Amazon, has DRM been removed from them.
I've never used K4PC to try opening a book other than downloaded from Amazon so not certain what you are seeing means.
You may want to try doing a calibre portable install and see if you still have the same issue. If calibre portable works, you could then do an uninstall of calibre and then re-install.
This discussion might be better taken to the calibre forum though enough calibre users in this forum, that it may not matter much.
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