Steven, i get that sometimes too man. mine comes and goes though. I also have noticed when i put a new (hot) Battery in its worse.
When the sus is on, the neck pickup (as far as it being a true PICKUP is concerned) is essentially off. So your hum is coming from the neck pickup when its being used as an active pup.
Also, on this same subject, when i am experiencing this hum, if i turn my sus ON, in any mode, and put it on a clean channel, its mildly distorted in a really bad fuzzy way. Its almost as if a new battery makes the whole thing too "hot" so it hums. Im not sure really. Messing with the pickup height of the sustainiac doesnt seem to affect it much/ if any.
This problem is also worse when i use wireless systems. The hum is far more pervasive, again only while using the neck (or both) pickups.