Post a short sample of the "waves" and someone might be able to suggest what is causing the problem.
I suspect this might refer to the optical image stabilisation of the Sony 550/50 camera. This actually is quite good, but, you can select a lower level or turn it off entirely. The image stabilisation works well under water too. I shoot single-handedly because I light the scene with my hand torch. If you go to the end of this (rather long) video, you'll see my Sony MC50 in an Aquatica housing counterbalancing the waves rocking the boat.
On the original topic, I used editing studio color adjustments to get rid of the excessive green bloom when my camera was facing upwards. This video was shot last year with auto white balance (pls don't laugh). More recently I have preferred to set the camera to a fixed White Balance - Outdoors, especially when doing video in darker waters and I am using a LED torch. Or, I set MWB in a shallower depth and leave it there.
The video was shot at auto focus which works quite well as long as a) there is enough light, b) the lense and dome is clean and c) nobody shines his/her torch into the camere. Later, I have started routinely setting the manual focus at the beginning of the dive. With the Aquatica housing this is very fast. Just point the camera at something a meter away (3-4 ft) and a single click of the manual lever is sufficient.
