Is there an alarm (orange or red) in the PFD on the Flight Data page?
Make sure that the flight modes you have selected are all valid for the CC3D. Maybe reduce them all to Stab1 (Att, Att, Axis, Manual) without Assisted Control (for a test).
(Also, I have a Nano that does not save settings sometimes. If you have a Nano, maybe look at the Configuration tabs and see if it looks correct. For instance, Input and Output should have some non-default numbers.)