Since I'm the one who started this thread, I believe that a little update is needed
After a few test and tries, I'm pleased to confirm that:
the syncing is now working with version 3.0 (and 3.01)
What I did was simply to start again from scratch, deleting the old files and then copying them again on the /Library/eBooks/
Make sure that they are in the mobi format, that the field (501) CDE is set to "EBOK" and the (113) ASIN is filled with the proper Amazon Asin code.
Copy the same file on all your devices and... enjoy perfect synch for all your books