All sorted now

Copied the Linux save file, Used a Windows install and copied the save file over, it loaded fine, quit out of the game and let Steam sync, re appeared on my usual Linux install and worked fine.

Guessing it was some odd Steam sync issue, back to the factory!!

I've launched Factorio which updated via Steam, my latest save file is no longer available to load, I can see it in /home/gareth/.factorio/saves, just not on the main menu. Not sure if this is Factorio or a Steam cloud issue. Is it possible to launch from the command line and force it to load the ...