After a monumental battle to find the right Segger software to use for the SAM4S16 Xplained (the online documentation points to the wrong place!) a day later I finally managed to find and install the right software from Segger.
I then tried to run AS6 to connect to the board. It's nice that the interface is almost exactly the same as using ISP/JTAg with AVR so I knew where to look and what to do.
Using "Device Programming" just to make sure I could contact the SAM4S Xplained I repeatedly could not connect. I just kept getting "wait for 1 more minute?" messages and finally timeouts with no connection.
In exasperation I thought I'd try closing and reopening AS6 and as I closed it down it was only then I found a message box saying that it had spotted the Segger debugger on the SAM4S Xplained and that the firmware was out of date and should it update? As I was closing down AS6 it was too late to use it at this point. But on restarting AS6 I went through the same sequence of trying to connect but once again the firmware update message box was "hidden" in the background and because the "Device Programming" dialog is modal there'd no obvious way to switch to it. However using Windows "Show Desktop" and the fact that the firmware updater seems to have it's own window I was finally able to access it.
This should NOT be this complex for a new user. As soon as the connection recognises that it cannot continue until the firmware has been updated it should cancel the Device programming modal dialog before showing the "update firmware?" messagebox.
This and the fact it seems you almost went deliberately out of your way to make it impossible to find the Segger software would probably have put me off using this Cortex M4 eval board if I wasn't so determined to use it. (I have 3 others from other manufacturers on my desk and could easily switch).
Not a good start. However...