The issue I had with an incorrect 1099R was for last year's tax, but I still remember the following:
1. Once financial institutions finalized and sent out the paperwork they will rarely go back and correct it. I spent much time escalating the matter within the institution until I realized it was a great waste of time. An individual issue will not carry much weight once their books are closed.
2. I actually called up the IRS. The hold/wait time was very long, but once I got someone on the line, he was most helpful. The IRS works on the same information sent to me, in my case 1099's and 5498's for Rollover transfers & contributions, and Roth conversions. He traced out with me where all the funds mentioned on the 1099 went and if, at the end, all the funds movements are accounted for, and match the amounts in the 1099's and 5498's, the IRS is satisfied. He advised me on how to proactively explain in the return the manner in which 1099 classification was incorrect. Even with time spent being on hold, it was the most productive time I spent preparing for last year's tax. It really changed my perception as to how helpful the staff at the IRS could be.
