I'm no expert by any means. Though I just got done building my 383 and I bought a eagle crank and went to internal balance it and it would of cost me 200 or so worth Mallory metal to get it right and a ton of holes in it. I called eagles tech line and complained to them about the internal balanced crank I bought. The more or less told me that I would have to run some TRW forged pistions instead of my Wiesco's. So I instead external balanced the assembly with no real problems.
It sounds like your machine shop tried to internal balance instead of external balance your assembly.