I've had the exact same thing as Custom happen to my D1s. The flash tube design shortcoming/flaw was not addressed in the D2, which is why I did not upgrade to them. SEA&SEA's explanation to me was [paraphrasing] "we are very sorry but this can happen because the flash tubes are those taken from conventional land based flash units and simply housed in an underwater housing (sealed, traps heat) - we do not have the resources to design from the ground up a flash tube assembly just for this strobe". They told me not to fire them 10 times at high setting 'in a row' and that if I did I had to wait 10 minutes for them to cool down. It does indeed say this in the manual of both the D1 and the D2. However, when I asked them "ok, what about 12 shots at 80% strength - what's the cool down time there?" they said they couldn't answer and to just use my best judgment in not rapid firing them like I must have to burn them out.
I never had this problem with the YS-250PROs and I'm really hoping they come out with a redesigned successor to those or that they address this shortcoming in the next iteration of the D2. An underwater strobe should simply not overheat from usage or rapid fire (running out of juice is understandable). At least that's what I think as someone who has come across a baby whaleshark and a completely white manta on the same dive