I'm having the same problem and I didn't have it last week when I uploaded two books without issues, so this isn't because the ISBN numbers are too new. I purchased a block 2 weeks ago and this is the 3rd number from that group that's causing issues.
Basically when you click "Publish" in ibooks author, everything goes fine. When ITunes Producer opens up, and you begin to enter the information, as soon as you enter the ISBN it will change your vendor ID. When you add the Book title, it erases it and greys out the field. There is no way to get it back. Put the curser in another field like the subtitle and suddenly that becomes your Vendor ID, which is invalid.
Try a work-around by choosing to manually upload without the iBooks export by creating an export file and manually entering everything and the ISBN doesn't get changed, but the book gets rejected saying it wants an ibooks file (which is what it is) and won't allow for delivery. Same for the sample version which is created according to iBooks instruction.
I tried uninstalling and re-installing iTunes producer; doesn't fix the situation.
I tried uninstalling and re-installing iBooks. Doesn't fix the situation.
This problem did not exist November 1 and November 4 when I uploaded two other media rich books, which are currently on sale in ibooks. The bug has occured since November 4 and it's preventing books created in iBooks from being delivered. I've sent several SOS emails to apple. Still no response.
PLEASE APPLE FIX THIS!!!
I cannot afford to spend another month reformatting this book in InDesign to create an epub for what I already created for APPLE in iBooks. I doubt anyone else can either.