You are identifying the box incorrectly. It's box I2 (box [letter i] 2), not box twelve. If you identified the box incorrectly in your response to the IRS, perhaps the IRS misunderstood your response.
Also note that the Schedule K-1 must have the EIN of the IRA custodian as the partner's identifying number. It must not have your SSN. The name of the partner should probably also include the phrase "Roth IRA" such as "[Your Name] Roth IRA." If the preparer of the Schedule K-1 did not prepare the schedule correctly, find out why and obtain a corrected Schedule K-1.
