Playing with my YS-01 and Olympus E520 this morning. The way the Oly Auto ISO works is that with flash on the ISO goes to 100 regardless. With flash off the camera picks a suitable ISO for the exposure (within the bounds of a menu settable High Limit). So my Oly wouldn't bugger with the ISO in flash mode but as you say, Intercepter, we need to see the OPs exif data to get a handle on what his NEX has done.
My test was in a very dim bedroom shooting white objects at 20cm with a macro 50mm f2 lens (100mm equiv) on a white bedsheet (I thought this was as challenging as I could make it).
I first tried with the built in flash (the shutter goes to 1/100 when flash is on in Auto/P/A modes).
F2, 1/100, ISO100, Auto Flash - white out.
F2.5, 1/100, ISO100, Auto Flash - blown highlights
F3.2, 1/100, ISO100, Auto Flash - no over exposure above this F-stop
Then with the YS-01
F2, 1/100, ISO100, TTL max - white out.
F4, 1/100, ISO100, TTL max - blown highlights
F5.6, 1/100, ISO100, TTL max - no over exposure above this F-stop and exposes all the way to F22
So the YS-01 on full power contributes nearly a 2 stops difference to the point at which you will blow the highlights. I did some further tests, reducing the flash power control (Sea and Sea say that in TTL mode this is dimming the flash) At the half power mark (two clicks off max on the YS-01 control) the results became like the set from the built-in flash. At 1/4 power it became very dim so I upped the ISO by two stops to 400 and again got the same result. So it seems that going half power reduces the blow out point by 2 stops and at 1/4 power another 2 stops.
It is important to note that I was only testing for the point of blown highlights. Once I had reduced either the aperture or the flash power or the ISO enough to prevent the over-exposure then there was no further difference (i.e. it didn't get darker and darker) because the camera and the strobe were working in optical TTL unison to expose correctly. Which is what the OP wants of course.
Of course this is a different body and lens to the OP and it wasn't done underwater but I felt I educated myself a little and the results might help diagnose what is happening with the OPs shots.
Simon