Sticky:
How to ask a question about conversion problems
The internal file structure should not make a difference, as the specs permit the files to be anywhere. Only be convention (to make things neat, it became a habit among many) do the files go anywhere particular -- the only hard requirement is the content in META-INF.
If calibre converted it, it should work under most circumstances, but there may be a bug with your device's firmware.
It is possible the Bookeen subforum would know more than us.