Looks like my main problem was some working directory locations. First time I installed, I put the program in D:\autochart. I noticed this broke the default map and other things. So I reinstalled to the default path. When looking through settings, I saw lots of paths pointing to the old dir that doesn't exist anymore. So fixed a few I saw and at least I get the green boxes of my mapped areas on the home screen.
Just need to figure out how to map all of the green boxes at once and maybe it will fix my problem.