Okay I'll tell you what I did (and just tried again now following your instructions) so hopefully this will help?
I turned on the Ebookwise, then opened the EBWLibrarian. Clicked 'Create New' and selected a book from a folder on my computer, filled in the name of the book, author and category. The format is automatically--and I double checked it--as you said, "GEB1150 (Grayscale Half VGA)"
Uploaded it, said upload was successful and it appeared on my bookshelf on my computer. However, I look at the format it says the book is there (on the EBWLibrarian) and it says 'eBookwse 1150'. I believe this could possibly be the problem? If so, how do I change it? I've tried uploading the book as 'eBookwise 1150 (default)' as well and it doesn't change the format etc nor any of the problems I'm having..
I can view the book as it would appear on the eBookwise, from my computer, so it's not protected. I can upload the book as a word doc, rtf, any of those and it doesn't change anything.
Thank you so much for your help so far, looking forward to more replies so I can finally get this sorted!