Thanks for your info Oafaloaf, it's handy to know that all that messing about isn't going to fix it.
Having contacted the elves at Origin's chat service, I've tried waiting for an update that never arrived or didn't work if it did. Repairing the game. Disabling Origin in game, and finally, a clean reboot. All to no effect. I've also tried System restore, still no solution.
There is definitely something strange about their saving system. I have found that using the chapter select helps, though it will start you at the beginning of said chapter, so it can mean a lot of repetition! Also, it may be that part of my problem is having purchased 'Awakened', coz in my chapter select section, it seems chapter 19 is the final chapter of the main game, and it felt like it too as I got to the part with the boss monster with yellow eyes that you have to fire markers at, whilst restricted to a small disk that's constantly invaded by Nec's! That's where I kept dying, and after 5 or 6 restarts, I just got bored and frustrated so would quit, expecting to restart at the lead up to that fight, but instead it would restart me at the openong of Awakened. Now, I notice that in the chapter select section, Awakened is listed as chapter A1, immediately following chapter 19 of DS3. So, it occurs to me that maybe the game figures I've done enough in chapter 19 to count as finished!?! The reason I think this, is because in the Awakened folow on, it's given me all my resources, weapons and rig and the last suit I chose from DS3 main game! It seems to be the equivalent of New Game +, but when I've selected New Game + it tells me that I must complete one playthrough to access that?!?
All very weird and confusing, but I've decided to just play Awakened and leave the actual end of DS3 for now, as I've got all the gear I need to stand a chance in Awakened.
Don't know if you've got Awakened, or if any of this is useful to you, but it may prove useful to someone out there struggling with this overly complicated game!