Some possibilities spring to mind.
1.) That high up, Endermen may not be able to pathfind to it, and so ignore it as something they can't hit anyways. Try putting it at ground level and giving them supposedly-walkable paths to it over open trapdoors and/or signs.
2.) I seem to recall that Endermen ignore endermites spawned in with a spawn egg or commands, and only attack naturally-spawned endermites produced by them teleporting or a player using an enderpearl.
3.) They also need to be able to see it. I don't THINK the walls of the minecart block their view, but putting it at ground level may also fix that problem if it's what's going on.
Hope this helps.