Canon 6D won't reliably focus-lock Wazzup?

So I can't get my new-to-me 6D to focus lock reliably. The configuration:
Ikelite with 4-Lock port and dome
2x Ikelite strobes
1 Focus light
50 mm lens

The camera has no problem out of the housing with achieving a focus lock (green LED is solid), but underwater, I can get maybe 1 out of 4-5 shots.

I'm in Raja Ampat, with very good visibility, so there should be sufficient ambient light. With and without the focus light turned on, I have the problem

Could this be a firmware problem on the camera? There are < 8K clicks on the body so I believe it is "like new"

Any suggestions are most welcome

What specific lens and dome are you using? If the lens is not a macro lens, and your dome is small enough, it's possible that it can't focus close enough to work with the dome without a close-up lens.

Yeah, dome or flat port?

As Barmaglot says, if a dome, could be that the lens can't focus on the virtual image that the dome creates and where the lens needs to focus - rather than on the actual subject. As he says, a close-up lens should help with this.

If it's a flat port the lens needs to focus on the actual subject. If you are using a flat port, is it possible that a slight misalignment of the camera in the housing is causing pressure on another control button that is preventing correct focus operation? Are you getting any other slightly strange operating issues underwater?

Thank you and Barnaglot for your replies.  Clearly I need remedial help

I'm using the Ikelite 8" dome and stock extension. The 50mm lens has a 1.5 foot minimum focusing distance

Can you please expand on the virtual image?  Im moving from a compact with wet lenses and never had to deal with this stuff

Thanks again

Ikelite's port chart for FL system is here: https://docs.ikelite.com/reference/port-chart-fl-system.pdf

If you look at the top of page 8, it lists three different Canon 50mm lenses, all of which require a +4 close-up lens to work in a dome.

Basically, the boundary between water, glass/acrylic and air refracts light and functions as an additional lens element in front of your lens. Google 'dome port optics' for detailed explanations, but the gist of it is that for a subject at an infinity distance, it creates a virtual image at 3x the dome's radius away from the dome's front. Modern lenses typically focus within 25-30cm of the camera sensor and thus work fine with most domes that are not too small; older lenses - such as your 50mm - typically have minimum focus distances of 45-50cm or more, and thus frequently require close-up lenses in order to function in a dome port.

Like they say. . . "That's your problem right there Vern"

Many thanks for your help. I've been beating my head against this for too long.  RTFM is something I too often overlook

1 hour ago, JohnN said:

RTFM is something I too often overlook

Problem is that there is often no manual for this stuff. But then that's why there is Wetpixel! The learning curve for most of us (all of us?) is massive and it takes time and patience to get your head around it all. 

So just ask away..... I always felt there was no such thing as a stupid question. It's the answers that be stupid.