have you cleaned out the system lately? you should deffinately get an air pump, but its an aeroponic system right? so the roots arent submerged? if so i dont see how that would effect it... sorry that wasnt much help.
dude if the stone in the aerogarden isnt working any more thats your problem, you need the stone to airate your water, without that here isnt enough oxygen in the water to support good root growth, this is a great way to get root rot fast... get an airstone in there and it will fix it...