SQL Server Configuration Manager is not applying permissions

I am trying to change the service account of an SQL Server 2014 instance to use an MSA. The MSA has already been created and installed to this server. I have changed it to a domain account previously and this worked fine. Configuration manager comes back with "Process terminated unexpectedly" when it restarts the SQL Engine. Checking the event log I see messages about not being able to access the error logs. When adding permissions to the error log there are then messages about not being able to access the master ldf and mdf. I've never seen this issue previously, so I'm wondering if anyone has seen anything similar? OS is 2012 R2 SQL is 204 EE