I just bought and am in San Pedro using a Nikon D70 and SB800 camera in a Fantasea housing.  All the flash pictures are very underexposed.  I used the housings above water and am getting the same under exposed result.  I took the camera and flash out of the housing and took a picture (camera and flash connected via the housing connections) still under exposed.  When I connect the flash directly to the camera i.e not use the housing or its connectors and do not make any setting changes the pictures are fine.  Thus there is nothing wrong with the flash or camera.  I am completely perplexed.  I have one day left of diving.  Any help would be greatly appreciated.  I am not able to contact Fantasea.

I do not have the set up you have, but have run into similar issues and perhaps this can help trouble shoot for the last day. Not sure what settings you were using, it sounds like the flash was firing (?) but not at the proper time.

For instance if TTL/iTTL was not working properly for some reason (cord, bulkhead or other reason), the strobe can dumping a full flash on a pre-flash of the camera so when the shutter is released there is no power for the actual flash and the pictures are underexposed. Also could happen if your camera was set to iTTL and the strobe set to Manual.  So double check to make sure all the settings are correct (sounds like they are probably correct since you indicated if the strobe is connected directly to camera it is working properly)

On some setups turning on the strobes first then the camera can help with the issue.  So I would test in both combinations to see if it works that way.

You can also just shoot the camera and strobe in manual if the iTTL is not working properly and then take a look to see if the shot is over/under exposed in the screen and adjust accordingly

The manuals are here (just in case)

http://fantasea.com/manuals/FD-70_manual.pdf
http://fantasea.com/manuals/FD70N_Manual.pdf

Keep us posted with the solution!
This issue sounds interesting.

Did you also check if you can see the strobe ready
light through (little flash sign) the viewfinder?

If you can measure the pins in the strobe connection
you might find a wrong pinning of the cable to fix this
strange behavior.