If you only have MobiDeDRM.py version 0.01 or 0.02 then yes, that sort of thing can happen where it appears to run with no error, but the resulting eBook is hosed. Only 0.04 has so far not had any errors that I know of.
So if you have 0.01, you also need 0.02 and if you have 0.02, you want to find the thread here with the patches to apply to convert 0.02 into 0.04.
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