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Newly painted fabricated bed rusting on welds under paint

I painted a friends wrecker about 1.5 months ago, He had a new bed made for it out of tubing and steel diamond plate. He brought the truck to me after the bed was finished and I cleaned all the new steel with wax and grease remover then 2 coats of epoxy primer, 2 coats of bed liner and 1 coat of clear. I was at his station this evening and he says the weld that are on the inside rails of the bed where the diamond plate is welded has rust coming through, This was all new steel and was wire brushed by the guy who made it. My question is what has happened and how can I fix this? I was shocked to see the rust coming through the welded areas, Any help is greatly appreciated.
Man I went over that truck time after time and really took my time to do everything right and the next thing I know the phone rings and he says hey man the paint has rust coming through. I had another painter friend to go look at the truck and there she was unwelded seams with rust stains running out. I said hey if the fab shop had took as much time and care as I did you would have less a headache.