Hi mate, thanks for the response. I've just lifted off, looped around to waypoint eight and landed and indeed scored 65 points but, unfortunately my progress has not been saved again. I'll definitely find a suitable place to post this elsewhere on this ED forum in case there is a wider issue that somebody might be aware of.
I'm running the latest version of DCS on Steam and waited to make my fourth attempt at mission two once the recent update had been released. I have never downloaded any official mods for fear of this sort of thing happening.
I'll keep plugging away with the campaign though and have enjoyed what I've experienced so far.