I had an issue like this. I'd set my work environment, update everything to a new scheme, and save it as a new profile. Then I'd go right back in, and two of them (I think palette schemes and one other) seem to reset themselves to custom. I reported this, and Graphisoft mentioned it's a bug. They don't actually change, they keep your settings, but the name goes to custom.
So if your settings are ok, but just the name is changing, then it's a small bug they don't seem interested in fixing. If your settings aren't staying the same, then it is some other problem.