rcgagar -
The only problem with specifying a "rigid diaphragm" is that it is so easy to forget it's there and it will cause the beams at that level to have zero axial force (because the diaphragm is so much stiffer in that plan than the beams).
I would suggest just throwing in a few X braces to halfway represent the diaphragm where you connect some of those gravity only columns back to the lateral resisting frames.... Just to get lateral stability out of the way.
You have a number of other issues as well related to rotation at some joints. Those are much more minor and can be fixed per the suggestions from Jayrod12.
1) change all column end releases to fixed-fixed
2) change all pins at the bottom of the columns to include Y-axis rotation as a reaction. You can look at the end to see if it's restraining any torsion and address that situation as required.
Just to elaborate on item number 2: In a 3D analysis a column that is supported by a "pinned" boundary condition at the bottom and is connected to beams with pinned end is technically unstable for torsion. You and I (as reasonable engineers) know that there isn't any way for torsion to get into the column. But, the program isn't quite smart enough to know that all it sees is a zero in the main diagonal of the stiffness matrix and it wants to find a way to correct that instability. That's why we often add an additional rotational restraint about the global vertical axis (Y in your case).
Note: I corrected a (very) minor issue in Jayrod's response when I quoted him. I changed his reference from "y-axis" to "Y-axis". In RISA, they use the lower case x, y, and z to refer to the local axes of members and plates and such. Then they use the upper case X, Y, Z to refer to the GLOBAL axes of the model. In all my years working there, I never asked why Bruce / Roger did that. It seems to me that it would have made more sense to use X, Y, Z for the global axes then something totally different like 1, 2, 3, or i, j, k for the local axes.
None of us work for RISA anymore, but I still talk to Roger, so maybe I'll ask him one of these days.