There always seems to be confusion re rail passes and ferry companies. Things change on a yearly basis but I believe this to be the state of play for 2004. This is lifted from the official GNTO website. Hope it helps.

Your rail cards are accepted in Greece, only by Superfast Ferries
and Blue Star Ferries on the Italy-routes.
Please note that booking with cards in advance is not possible.

Cards are only accepted at harbour offices on the day of departure.
The passes are not valid for Greek Island routes.
Inter-islands passes are not available. (In conjunction with rail cards)