Your post is vague as to the precise timeline and what specific steps you took and did not take on what dates. This makes it difficult to evaluate your situation. A qualified professional armed with all of the relevant information and documents should be able to help you in a timely manner.
My paperwork was not on hand when I made the post, but I have it in front of me now.
02 MAY 2014: Contributed $5500 to a Roth IRA
03 FEB 2015: Re-characterized $5500 Roth IRA contribution from 2014, plus gains, as a traditional IRA contribution.
29 FEB 2016: Received Notice CP2000 from IRS, notifying me that I underpaid taxes because I claimed an IRA deduction of $11,000 (mine + my wife's), but only $5500 was deductible
18 MAR 2016: Sent response to IRS after confirming that my 2015 Form 5498 properly documented the re-characterization in the previous year.
16 MAY 2016: Received another Notice CP2000 from IRS, which had basically the same wrong information on at as before
15 JUN 2016: Sent another response to the IRS, this time with a statement from my broker which confirmed that the re-characterization was properly documented and the pertinent forms were submitted to the IRS
Last Month: Received another Notice CP2000 from the IRS, along with a letter that completely ignored any mention of the re-characterization and re-iterating that Roth IRA's are non-deductible.
For reference, my AGI in 2014 was 70,532 in 2014 (Married Filing Jointly) - nowhere near the cutoff for a deductible IRA.
I will take bacchi's advice, and send the documents over again until I get a competent employee to review them. I think I may just send the same documents every day for a week to improve my odds.