Hi,
We saw your screenshot but it doesn't give enough information to be able to say what the problem could be.
For example, it could be that the "access level" of your manual shipping plugin has been changed to something else than "public" in the Joomla plugins manager, which would remove the shipping methods of that plugin from the checkout.
So please check each point of the FAQ.
If you didn't find the issue by checking each point, please provide instructions to reproduce the problem and screenshots of the settings of the shipping methods (not the listing, but when you edit them) so that we can have a better understanding of the situation.