ACI 21.6.1 Requirements being applied to Gravity Columns?

I don't have a moment frame. The building is designed for Shear Walls but we are in SDC D. Do you have to assume you have some sort of Moment frame in RAM?

And also, i don't see anywhere in 21.13 that references 21.6.1.1 & 21.6.1.2 which is the section RAM is telling me I am violating. It says the column does not meet the dimensions of 21.6.1.1 & 21.6.1.2?

A shear wall structure in SDC D still needs to have the gravity columns checked against 21.13. Presumably the design displacement in such a structure would be smaller than that of a Moment Frame structure, however.
The link from 21.13 back to 21.6 should start with 21.6.3 however. I don't see any reason for 21.6.1.1 to be checked on gravity columns. Make sure your frame type is correct (ordinary moment frame in your case) and confirm if you are using the latest version 15.03.

A shear wall structure in SDC D still needs to have the gravity columns checked against 21.13. Presumably the design displacement in such a structure would be smaller than that of a Moment Frame structure, however.
The link from 21.13 back to 21.6 should start with 21.6.3 however. I don't see any reason for 21.6.1.1 to be checked on gravity columns. Make sure your frame type is correct (ordinary moment frame in your case) and confirm if you are using the latest version 15.03.

Don't all buildings that are SDC D need to be special?

Yes, and I assume you will use Special Concrete Shear Walls when you get around to the wall design, but since you don't actually have any moment frames I wanted you to test using the Ordinary Moment Frame option to see what happens in relation to the gravity columns.

I've actually reproduced your symptom in a test file. I'll report back when I understand the design flow better.

and I just ran as ordinary results "Story 1
* Column section dimensions are not acceptable per ACI 318-11 Sec. 21.6.1.1"

I did some further review and here's what I observed. The gravity columns are getting checked for Section 21.6.1.1 only when Pu > Ag*f'c / 10. We get here via 21.13 -> 21.13.4.3. 21.13.4.3 references section 21.6.3, 21.6.4, 21.6.5 and 21.7.3.1 but NOT 21.6.1. I will file a defect to have 21.6.1 and 21.6.2 exempted for gravity columns. In the meantime, if this is the only failure or warning on your small columns it should be fine to use them.