Greetings Geokhentix:
Are you choosing a different folder for your decrypted book? Are you sure that it is infact the decrypted version that is getting added to Calibre? If you get a successfully decrypted response from ineptpdf, then the new ebook that you are creating should be drm free. Might want to give it a slightly different file name so you can keep the two files separate.
cheers
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