Nathan, we have new GPS checks whilst starting up now. Do you have arming checks and arming enabled? I very strongly recommend you do. You will note you can't arm for a few seconds (about 10) after startup whilst the Rover gets its GPS lock sorted out.
When you say you saved the configuration file and that didn't work what do you mean? You couldn't save it from Mission Planner?
If you had a log file you could send (or a link to a dropbox/google drive etc) that would help enormously.