Can you post a pic? Your rear shackles shouldn't move that much - even off road. Not enough to allow that bolt going thru the rear spring eye to come up and contact the unibody or shackle box. It's possible the pass. rear bolt might be hitting the exhaust but other than that, there isn't anything that should be anywhere close to being in the way of the shackle bolts. I think it'd also be obvious as to what's hitting by looking for clean metal scraping anywhere around the travel range of the shackle.
If your leafs are longer than stock, you might want to look up at the bumper mounting bolts - one of the lower bolts for the bumper bracket goes into the shackle box area and I've had shackles hit that bolt when I've compressed the leaf pack/shackle off road......... :dunno: But I can't imagine driving around town would allow enough movement to have your shackle hit that bolt either.