Thanks for the responses. So I tried the flight again, just to make sure, and had the same issue. I then tried it in the default Cessna 172 G1000, and had the same problem. I then did it again, but in the default 172 without the G1000, just the GNS 530, and that time it flew it correctly. So this is just a G1000 problem. I contacted Laminar about it, we'll see what they say.