You are correct, the payer has provided an incorrect Form 1099-R. Box 2a should have the same amount as box 1 as required by the instructions for Form 1099-R for this type of distribution. I can't imagine how the payer could have made such a mistake unless the form was manually prepared, which would be odd if there was nothing unusual about the distributions. An automated system should not have permitted such an error.
I would contact the payer again and escalate to someone there who actually knows what they are doing.
