Hi James,
Erich is right, if you have more projects, you have to open to proper one. The MCUX Config Tools allows to have just one configuration to be opened, so if you have more Eclipse projects, you have to explicitly switch/select the project you want to work with. Either in the Config Tools perspective as Erich proposed, or in the Develop perspective, in the Project Explorer view:

or even popup menu on the project folder.
Regards,
Libor