Yep. When i bought my truck there was a little rust on the driver side rear fender and under the driver side ext. cab window. Now both fenders are rusty, both cab bottoms are rusty, tailgate is rusted out, front fenders are starting to rust, and the doors are starting to rust. Freaking sucks but normal here.
I'd say your best bet to fix it completely is find a CLEAN southern bed, strip it down and clean it up, seal it, paint it, and work on the inner fenders so they don't hold moisture. I've seen a bunch of trucks with rust on the seams of the new patch panels around here, either people don't seal it right or the seam attracts moisture or something. :shrug: