The current build of Mystcraft does not work for 1.6.4. This is because vanilla structure generation changed, forcing many mods to update.
I have not yet had the chance to actually do anything with Mystcraft since before 1.6.4 came out, so there is not yet an update to it.
I hope to get he opportunity in the very near future. I will release an update for 1.6.4 in order for people to transition maps properly.