ok im not 100% on this but it seems that the people that are having problems with thier springs are not using quality springs.
I ran pro comps on my truck for about 6 months and after the 6 months the were trash. they would reverse arc under flex and were bent all the hell. my truck had all kinds of problems including the shackle problem you are experienceing, along with my truck sitting uneven i even broke one towards the end.
I understand its difficult to come up the green to buy marlin, or all pro because i couldnt afford it myself.
but what i did was go back to a stock spring add a few leafs from an f250 and run 3 inch blocks. i ended up with abot 4 inchs of lift. then i ran 6 inch shackles and cut the bottom of my truck off.
Its a little redneck
but it works well. i have great flex and more then enough clearence for rocks and my 33in tires
just throwing the thought out there good luck