I recently received HHKB Pro 2 (model PD-KB400B), and I'm having some issues getting it set up in Ubuntu 14.04.
The main issue is that the meta keys aren't producing the meta keycodes -- rather, they are producing muhenkan and henkan used for Japanese input. Since I got this keyboard primarily to use with Emacs, this is a bit of a bummer. A secondary issue is that the tilde key is generating 'escape'. Pressing shift+tilde does produce a tilde, but that leaves no way to enter a back tick.
I've tried various switch settings, but haven't had any luck. I also tried changing the keyboard layout in Ubuntu using the settings manager, but so far that hasn't worked out, either. I've read conflicting information about using xmodmap or xkb to remap the keys, but haven't gotten anything to work. Right now I have all the switches in the 'off' position.
Is anyone using the HHKB in Ubuntu 14.04? If so, care to share your configuration? Are there firmware differences between Japanese and US models? So many questions ...