Here's a long shot to consider. I don't have a D800, but do have a D500 and I assume that the menus are similar. If the delay is consistent in length, there is a setting in Custom called Exposure Delay Mode. It's d5 in the Shooting/Display menu on my D500. I's assume that it's also on the D800.. If that is set to other than off and is somehow getting triggered while UW by pressure, that may cause the problem. This is different than Timer Release. Like I said, this is a real long shot.
Also try this. Make sure that you're using AF-C focus mode and set the a1, AF-C Priority Selection to Release. This will cause the camera to fire without the need to achieve focus. If this eliminates the problem, then the camera is, in fact, waiting for focus before firing and, for some reason, it taking an inordinate long time to get focus.
Like the others have said, misalignment is the most likely cause. The trick is to figure out which button is getting pressed to cause the problem.
I'm not familiar with the S&S housings, but I had an old Aquatica D70 housing that had plastic thread protectors on the end of the rods used to activate the buttons. Occasionally one of those protectiors would work itself loose and contact a button before it was intended to do so. This drove me crazy until I figured that just a slight amount of sea pressure on a button would cause contact with the button when the protector was slightly out of place.
Reef Photo isn't too far away. Consider taking the rig into them for a look.
Let us know what you find.
- MikeVeitch likes this