Interesting. Never knew about that... I guess I never had a need. I've done it a single document at a time and it works.
Here is an idea, but it is a long shot. In some older versions of the FDK doc, there was a mistake where it said "GenerateDoc" instead of "StructureDoc", which caused the single doc conversion to fail. I see that the latest version of the FDK doc has fixed that, but it still says "GenerateBook" for the book conversion. I wonder if there is any chance that it should actually be "StructureBook"? Maybe give that a try. If that doesn't work, I don't have any other suggestions at the moment. I'm a bit tied up to try it myself right now.