As I said earlier the HHKB lacks a set of dedicated Win keys
I do not have Windows, so I can not confirm what ch_123 said that "The Meta/Command keys on the HHKB double as Windows keys when run under Windows. " earlier in this thread.
But according to
Wikipedia, he is correct.
And even if that is not true, you can still remap the keys manually. At least you can in every other operating system, so I assume you can in Windows as well.
EDIT: Whoops, didn't see your post there, ch_123! geekhack was down when I tried to post my reply, and when GH was back I did not refresh the thread before posting