[itimpi]

You could look up the Calibre command line interface options in the Calibre User Guide (in particular ebook-convert). When using the Command line interface you specify the input and output files explicitly so bypass the GUI completely. This may be more suitable for your needs?

You mentioned that the Calibre folder structure did not make seem to be consistent. It should always be of the form author/book/. You have probably got calibre set to look at the metadata in the book file (it can be derived from the filename) - and this is not set correctly which is why you get strange folder.

However as you mentioned, if using Calibre to manage your ebooks you probably should be accessing the eBooks via the GUI interface, and treating the calibre library as a "black box" so that the file structure is not accessed directly.