Now that's a new one, so, if you switch the new subtronic TTL to manual it doesn't work well? This isn't supposed to happen, I don't think, but I guess it would solve your problem if you remove the ready light pin (there are no effects on TTL as far as I know, so you can just remove it and leave it out).
yes, indeed, I think that was a problem recently when I was diving in Yap and Palau. I had another problem with one of the flash and the flash arm battery (Mike Veitch knows about it...) and therefore switched to manual shooting using one flash only. And sometimes, kind of erratic, my camera was kind of blocking (not firing, not reacting at all) until I switched off both the camera and the flash and after a minute or so it was ready again. But happened only sometimes...could not figure out what is was and was not aware that it might be the problem like described in this thread until I read yesterday this one again... so I will test again all kind of options next time diving (unfortunately not before April in the Bahamas with Jimmy...ha ha).
And for Subal, I am not surprised that they don't know... but I will check with Subtronic and will let you know