Update to this post
I replaced the SD card with a new 16GB card, Formatted and reinstalled all the setup files.
It did give me an error message of mismatched firmware versions although I could not find evidence of anything mismatched. I did reflash the entire package of 3.5.2 and everything now is working as it should.
I can now edit and save changes to the config.g file, As an extra did modify some of the macro files as well as they no longer dissapear.
I would mark this one as resolved.
Just as an additional information I checked the previous SD card in a windows PC, Checked it for errors and no errors were picked up. Still a weird problem but I am chaulking it upto a problem with the origional SD card.