I tried to fix this issue with v1.3.2 (there was some negligence in my code), plz check if it's working now.
Unfortunately I cannot reproduce this error yet - are you blocking some scripts from ebook-dl.com (Noscript)?
You are completely right with your observations, I already wrote some function to generate these correct download links for magazines and books. Journals and movies are not planned to be integrated into this script, because they are offered in a different domain/system.
Actually I got problems with non-zipped downloads, especially pdf files (magazines ...). Those aren't bypassed into the download manager, but opened with that included pdf viewer in firefox (by default). So you have to save them manually and go back to the downloads page - too much effort :)
That's why I didn't release the new version yet.