Seams are notouriously difficult to de-rust. The problems arise when the original factory paint/sealer cracks and moisture gets between the spot welds. The trouble with blasting is that it would not have got deep in between the two flat spot welded sections. A phospheric acid neutraliser would have helped as this would potentially find itself between the plates via gravity, however is not without problem in itself as if you do that, it is near impossible to clean all the chemical back off again with the result of possible paint reaction.
As VR said, if you paid good money to have it done, then talk to whomever did it. Are you sure that it is rust coming back again or is it paint reaction?
If it were mine, I would be tempted to first of all blast as you have done, then phospheric, then wash out with something like Bilt Hamber Atom Mac
https://bilthamber.com/product/atom-mac/
Please note that I have not yet tried painting over that combo, so would experiment before doing it for real!