In my very uninformed opinion, I think it's some type of circuitry problem. Have you tried plugging in clean, with no pedals? Different guitars respond differently on the exact same setup. I think you should try a process of elimination- try a brand new, quality cable, eliminate the pedals, see what happens then. Have anyone who can look under the hood and see if your pickups are wired properly?

I've always been lazy when it came to the maintenance of my guitars, but with a growing guitar collection, I'm slowly learning; recently, on one of my Strats, I plugged in, no sound, nothing. I removed the output jack and saw a wire loose. I googled for schematics just to be sure, and for a total of about $15, I got a cheap soldering iron and solder, and soldered the wire back on, and I was back in business.

Just hate to see you spend money on a tech when the problem is "obvious".