I popped off a mail to
support@bookeen.com about this.
And about something else as well: popup notes in Mobi ebooks are not displayed when they are too large to fit on the screen. Instead, the Cybook goes to the 'Scanning library' screen (the three dots & reader one) and drops into the library. Opening the book again leaves you at the last page synced to the bookmark file, which isn't always the actual last page read :-(
We'll see what develops.