I know that when I use RAM Structural System, we design the gravity framing first, using gravity loads only. Then enable the RAM Frame module. What I'm trying to say is that by the time I'm on my lateral analysis, the gravity design is pretty close to complete, save for any iteration coming from RAM Frame. But generally if you are just analyzing vertical loads, I'd not include braces for the intial sizing of your members. Certain analysis softwares are quirky and things have to be done in a certain order or fashion to get expected results. Depending what you're using I'd follow JoshPlum's advice.
Scott Shields
Ghafari Associates, LLC