i don't know what the 1493 cable is, nor do i know what you mean by intertwined with the ad20...so one of those might be your problem. however, i've noticed pops and clicks in my recordings with the jb3 before as well. however, in my experience i always try to do a disc cleanup and format before i go taping. for some reason whenever i do that, i never have pops or clicks. it seems that after i fill the hdd up aways, i always have problems. other people don't have this problem and never have to do anything...so i dunno. but i don't think it'd hurt it, plus it keeps the hdd clean.
granted, you don't always get the chance to do it, but i still try to do it as often as possible.