hopster, I vaguely recall some discrepancies between the manual and my board, when I set up my BH6 rev1.02 board. I have it in an AOpen HX45 midtower. Here's the pin assignments that worked for me:
PN1 - pin 1 is on the right as you look at it, pin 11 on the left. Pins 1 -3 are for the Power LED, my green wire went on pin 1, white wire on pin 3. If your case has a keylock, that's pins 4 and 5. Pins 6 and 7 are for the HDD LED, my orange wire on pin 6, white wire on pin 7. Pins 8 and 9 are for the power on, red wire on pin 8, black wire on pin 9.
PN2 - as above, pin 1 on right, pin 11 on left. Pins 1 and 2 are reset, white wire on pin 1, purple wire on pin 2. Speaker goes on pins 4 - 7, black on pin 4, red on 6 or 7.
Hope this helps.