I have the same problem with the Ebookwise Librarian software. It almost always crashes on the first try, but works fine after resetting. Imo this has to do with running old software [the Librarian] on a new [Win XP and anything after that] OS.
I run Windows 7 the 32 bit version, and to get the Ebookwise Librarian working I have to run it in compatibility mode as Windows XP service pack 3.
I don't know any solution for your "problem", like you said, after a reset it works fine.
If your Ebookwise Librarian should stop loading books to the online bookshelf [like mine did overnight], then you can use the workaround I described in the thread above.