[rebl]

I've performed a clean install of both Calibre 64 and portable calibre.
I've deleted all the files in roming/calibre and the install directory.
All the below is valid both for Calibre64 and Calibre Portable:

After more testing I've noticed that most of the books have the wrong path in the single book convert dialogue (except for the first one and I think I've manually changed the path for that one) and pressing the reset to defaults button in the lower part of the dialogue will reset from the wrong to the correct path (that is stored in the Preferences).
That might seem to imply that a different input plugin settings set is saved for each of the books and somehow each of them was using this set on its own, ignoring the Preferences, and using a path different than the one saved in preferences...