missing modules only when opened by the unreal engine shortcut

i have a C++ project,if i enter the project by the unreal engine shortcut(open last project on startup is enabled)then it says that modules are missing,but if i open by the .uproject everything works fine,why is this happening???is it supposed to use the .uproject instead?

That’s not the default behavior; you should check your Debug Console when compiling from the IDE to see if there are any error messages.