A lot of us have been having the same problem there is no patch for it yet but someone did come up with a kinda fix check out this forum http://forums.nexusmods.com/index.php?/topic/907923-apocrypha-miraak-bug/
There are few people who have had the same problem I find that he's not actually invisable but he is underneath the ground haven't found a fix for this as of yet though