Ah okey, thats the problem..
Step number 1.
shift-windows-amd64.exe account new
(copy the account that you got generated, dont loose the password)
Step number 2.
shift-windows-amd64.exe --mine --minerthreads 4 --shiftbase youaccountnumberthatyoucopied
The --shiftbase shouldn't be required as shift should use the 1st account you have created as the default, but yeah if you want to be 100% sure it's best this way. I'll add this to the wiki.