Just guessing here, but did you re-install anything recently that can conflict with eBook Publisher, like eBookwise/GEB Librarian, BookDesigner, etc.
If so, try to re-install the latest version (v2.3.15). If not perhaps even try going back to the older version 2.2.5 available
here.
Then, if that works, just re-install the latest version!
Also, are you sure ALL your ebook creations exhibit that ordering issue or just certain ebooks you are converting...