Forget I asked. I fixed it...
EDIT: Because a friend of mine JUST complained about ppl only posting THAT they fixed it but not HOW they did it, here what I did. :-)
I emptied the sd card, manually added a book to it AND THEN STARTED THE READER SOFTWARE... manually creating a collection on the reader might have worked as well. Looking at the internal db, it seems just adding the book leads to a creation of a new db but it does NOT populate the collection start id. that only happened after starting the software.