Illustrator save cancelling when followed by save as and saving a PDF

I'm suddenly having an issue with saving in illustrator. Once I have made a change and try to save over the original file (cmd+s) I quickly follow this by saving a PDF proof to send to clients (shift+cmd+s). This is how I have always worked but lately when I go back to the files the illustrator file has not updated. As soon as I am pressing shift+cmd+s it is overriding the original save. I have lost a fair amount of work due to this and I've never had an issue before.

I've spoken to adobe who say it is a computer issue and to complain to apple but I'm not sure about that and just wondered if anyone else had come across the same issue and had a solution before I contact them?

I know I can just wait to make sure the ai file has saved before making my proofs but old habits die hard and 100% going to lose my work again because of this.