It seems that there was a manual attempt to correct the transaction and they incorrectly adjusted the amount in box 3 of the Form 5498 upward instead of downward by the amount that ultimately went to state tax withholding. Bookkeeping adjustments like this are easily mishandled.
Although it probably would have resulted slightly different amounts of contribution basis and conversion basis ending up in your Roth IRAs, a simpler correction with far less chance for error would have been to simply request a regular distribution from the Roth IRA equal to the amount that they failed to withhold for state taxes and have that entire distribution paid to state tax withholding. With the exception of the possible shifting of contribution basis to conversion basis, the tax result would have been the same as you had intended.
Where you say "conversion amount requested," I think you actually mean "distribution amount requested." The parts of the distribution that you requested to go to tax withholding are amounts that you technically requested not to be converted to Roth, so are not part of the conversion amount.
