I am testing a the latest code on a CC3D and I don't get that problem.
You didn't mention that you erased settings, and that could be the problem.
If you need your settings, I would suggest that you use the old version of GCS to reflash the old firmware, export your old settings, and view your settings to write them down. PIDs, flight modes, roll rates, tweaks, etc.
Then use the new GCS to flash the new firmware and "erase settings" this time, right after flashing. When you reboot after that, you should run the wizards and manually enter PIDs, etc.