Obviously, I can't do a real thorough review of the model. But, there are a few things that strike me as strange. Not necessarily wrong, but items that I would look at closer if I were the supervising engineer and someone brought this to me as their model. Enough things that I doubt whether this model is a good representation of the structure.
1) What's the purpose of modeling in the 2x4's. That's little more than blocking, right? Not sure we should be relying on them to share load in the analysis. That's not necessarily wrong, just not something I would normally do. Plus, it seems like there are more of them in the model than in the drawing.
2) Area load mesh size is probably too small, especially for the old version you're running. It doesn't really make a difference in the version that I'm running. But, I think that is mostly luck based on the errors canceling each other out on each side. I would prefer to see a closer of 5.76in^2 rather than 144in^2 like it's currently set to.
3) Those 2x4's are laying on top of the 2x8 rafters, right? That's probably enough to consider Le_bend-top braced at each 2x4. But, I don't know if it is enough to brace the rafter for weak axis buckling (Le2). And, it is definitely not something that I would rely on for bracing strong axis buckling (Le1).
4) Your load combinations don't seem correct for NDS design. Those are all strength level load combinations rather than the typical NDS service level load combinations that RISA is expecting.
5) You have most of your members with fixed end conditions. That's possible if you have a steel beam with the flanges welded to the column or such. But, I don't know that you can create that type of moment fixity with a wood beam.