They were originally wired into a DIF dual fan controller, but the controller took a crap on me. It does however have a manual on/off switch that I have been using since it still works. So since the the DIF fan controller has relays built in, and it doens't work anymore this could be the reason that it is cutting in an out?
this is the controller I was using.
http://www.frsport.com/DIF-Universal...-B_p_8173.html