I have been a bit confused about the differences between the HHK, Lite, and Mac modes set by DIP switches 1 and 2 on my HHKB Pro 2. An earlier
thread on GH indicated that this issues was not confined to me, and the
Elite Keyboards mode configuration table does not explain why the meta key does not work as a Windows key in HHK mode (this is the same table included in the HHKB instruction leaflet).

I was cruising the Japanese PFU website and came across the configuration table above, which actually explains WHY the meta key doesn't work as a Windows key in HHK mode: HHK mode emulates a 101 key keyboard, which did not have the 2 Windows keys and the menu key which were part of the 104 key layout (emulated by Lite mode). Mac mode emulates an Apple Extended Keyboard II, which also features meta keys.
Here are links to the
translated and
Japanese PFU website featuring the table attached to this post. I hope this clears up some of the confusion associated with HHKB Pro 2 modes.