That seems to indicate that ebook-convert is somehow unhappy with its options. I assume the window behind the ebook-convert is the batch file output? Could you post that, please? (A hint: In a console window, right click on the title bar, select edit. There should be an option allowing you to select text. Copy it by right clicking on the selected text, the highlight should then disappear.)
Edit: My bad, never mind. Just tried the batch I posted myself. I made two rather embarassing typos. Try this:
Code:
for %%i in (*.pdf) do start /wait ebook-convert "%%i" "%%i.epub"
I'm sorry, I should have tried it before posting.
Edit 2: Also note that this will still not handle DOC/DOCX in any way.