It's very hard to troubleshoot based on such limited information. That said, make sure that the "status" of your envelope (especially fenestration) is what you want.. "Existing" for all envelope except those new windows which will be "altered" or "new" depending on the code definitions. It gets tricky if your replacement windows are larger than the existing openings because some portion of the window is "altered" and the rest is "new". CBECC software isn't great in these situations, and prescriptive makes a lot more sense. Note also that if you're using the performance approach because you can't comply prescriptively based on new window size and/or performance values, that's not going to change by simply modeling it. You'll need to expand the scope of the compliance model so that your envelope penalty is offset by lighting or something else that shows savings.