Thanks for the advice all - much appreciated!

Our Return flight was 8 days later - on past experience (from upgrading to silver), 3 working days is reasonable to wait for it to register properly.
But in this case it posted as 'Ineligible' on MMB the very next day, so we got straight back to BA to get it fixed, for precisely this reason. They told me that it was definitely their mistake, and that they are working to fix the issue so that errors like this don't recur etc etc...

This is probably what gave me a false sense of security that they would accept their error and refund us!