How can I override a virtual member function from base after updating to 4.1?

Based on your comment, this is the result of an API change in 4.1. AGameMode::InitNewPlayer gained a new parameter in 4.1, the const TSharedPtr& UniqueId. Even if you don’t use this parameter inside your override, the declaration in your derived GameMode class must match the declaration in the superclass.

Try adding the new parameter to your own InitNewPlayer function (both the header and the .cpp file), that should fix the warnings.