"Start Project" upgrade hangs system

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Attempting to create some code using the 'AtmelStart' gizmo. It would not allow me to add USB so I added the SPI and TWI that I'll need (using 'Start') and attempted to at least add the 48Mhz clock that will be necessary when I figure out how to add USB. The generated 'Start' code compiles and runs. When selecting "Re-Configure Atmel Start Project" I get this window which tells me that it has removed a software component: CLK, and added two OSC software components. Cool, I thought - but then this window will not go away, none of its buttons 'work' and I simply have to exit AtmelStudio altogether to 'recover'. The code is not modified to remove or add anything.

Anyone have any idea how to skirt around this issue?

Also, if I attempt to use 'ASF' (the 'ASF Wizard') it comes up with everything blank - Project: BLANK, Device: NO DEVICE and in the body of the window: "No project loaded", and yet there is!

Any help with this would be greatly appreciated! I'm trying to add USB with the ASF as the AtmelStart won't allow it. Having trouble making any kind of headway with these issues using this tool!

Image of AtmelStudio with 'Project Upgrade Summary' that won't go away