Sorry to hear this Steve.
I also have had none of these problems you have related.
Since I got my new computer and the "new" version of SH III, I have not experienced any problems at all.
I save when I want no matter what or where I am( underwater, under attack and in sight of enemy ships ect.). I save game often.
I keep my mods VERY simple and load them myself with back up.
From my experience, if you can, get a new machine with Win 7 and the "new" version of SH III and I think you will find alot of the problems are gone and keep the mods simple.
It maybe a case of few is better.
