I just had side rails put on my 03 silverado and now it sounds like something is twisting or bending underneath. any ideas on what that could be?

what do mean by side rails???

If you mean siderails as in nerf bars , it is possible that they have come a little loose or were not istalled properly. I do not know what style you have or if they install the same as the ones did on my 96 sierra but they bolted on using the existing body mount location and bolts. I would take it back to where they were installed or if you did it yourself, be sure that you put the ruber bushing back on the proper side of the brackets for the steps.