possible evil box glitch?

It doesn't. If you find a map it spawns in, skip the next map. There are a few exceptions to the rule, like Mushroom Castle and Stone Golems, but it works for the most part. Example: He won't spawn at "Outside North Desert of Ariant", but does at "North Desert Road 1", one map over. He doesn't spawn in the next map, Desert Road 2, but will appear at the Desert of Red Sand.

I'm with the idea that boxes are set to give you nice things for the first 25-30 boxes. Thats been my experience so far.

Now figure that out for Magatia, where the area he spawns in is 3x3 box lol
I've only found him in one map there.