Gessford.com is a good source of info for the machine work required to get a Shelby block ready to go. It's considerably more detailed and technical than an original iron block, which is no easy task itself!
I'm running iron heads (thus, 9.6), high riser's with BIG valves. Those valves won't clear the bore of a 428, gotta be a 427 if I run them again. I VERY carefully calculated and did a LOT of math (over and over again) to determine the exact proportions my custom pistons would require. It's very complicated stuff and it's NOT uncommon for folks to miss it "just enough" to end up with to much or to little compression. Piston pin height off or any number of variables. Perhaps, in this case, the piston supplier messed up, perhaps those pistons were exactly as spec'd. I won't make that call either way, just saying, it's not the first time I've heard of it happening. It's quite common actually....