Ok its not the actual fix that limelight provided which is causing the error. Even without the changes stock by attributes shows items which are in stock as not in stock on the checkout page.

I have temporarily disabled this by going to admin>configurations>stock>check stock levels - i changed the value to false so that customers can purchase. Im not entirely sure why everything is showing as out of stock when i have added the stock levels for each attribute -

If anyone can help it would be great