Hi Aled,
I'm a DBA, been part of part in supporting sharepoint deployment.
I have also seen the some situation the sharepoint upgrads which removes the Farm account access sometimes.
Where we have manually added recreated.
In your case, as its SQL WFC, the access will be same in each node where ever it runs. So please check if that something similar.
I would suggest to have conversation in Sharepoint Blog side as this is not really a person from SQL side can help.
And next time when you run just ran a trace or audit to the farm accounts alone for the access changes will help to identify the cause.