You might want to check the bridge. if the end which holds the E string might be too high. And it's ofcourse good to check the neck too, but I don't think that the neck is the problem.
Many Jacksons have a problem with their necks because they have been made out of two pieces of wood. If you check the back of your guitar's neck you'll notice the gluing (or how ever it is spelled) has not been made very wisely.