It would be my guess that the shackles are hitting the bed support, of which the fix would be to notch the support on each side to clear the drop shackles. On my fleetside shortbed, the factory stock shackle is directly under the support and if I were to install drop shackles, I'd most definitely have to notch the support to get them to clear. Can you post a picture of the area under the bed where the shackles hit so we can be sure of what you're describing?