Not just darkrai but a bunch of other legendarys are on the map. By the time I got to the haunted house I have found meloetta, keldeo, the clouds, the birds and I think shaymin, maybe a few others I forgot. And they seem to respawn after a while. But the game works fine otherwise so don't worry about it. About the slowdown on saving, it seems to save fine for me no slowdown here.