There is an issue where the default deployment, deployed.txt, can cause a crash to desktop from the deployment screen of a scenario.
After I unlocked the Rebels, I switched to them and re-made some of my designs with the same names, then went back to the deployment screen for the first scenario. It tried to load the other setup I had made with Federation ships, but trying to assign orders to the existing ships resulted in a crash. Selecting and deleting all existing ships or deployed.txt in the scenario1 folder solved the problem.
I think giving each race its own default deployed.txt would prevent this situation from coming up at all, and also make replays as different races a little easier.