The only thing I can think of offhand is that you may have started off creating your project using the generic File -> New -> Project function rather than creating a C/C++ project, or you did not create a C/C++ project with the Ac6 STM32 MCU type selected.
Make sure that when you start out to create a new project, you select File -> New -> C Project (or C++ Project), then in the dialog that appears, select/expand “Executable” in the lefthand “Project type:” list, then select “Ac6 STM32 MCU Project” under that.
After you enter a project name and select “Next >”, use the defaults on the “Select Configurations” page, click “Next >” again, and you should see the “MCU Configuration” page. Make sure on this page that the “Show ST NUCLEO boards” is checked (OK to have others checked, but this one at least must be set).
There won’t be any text visible on the “Board:” dropdown-list button, but if you click it, you should see a long list of (Nucleo) boards to choose from.
If you just installed the SystemWorkbench package, odds are that you won’t have the latest version of all the tools - this is true even if you downloaded and installed the “latest” installer file. Use Help -> Check for Updates to get the latest versions of the Ac6-specific Eclipse plugins and toolchain.