Changes to MySQL config used by docker container are not appearing in Circle CI Jobs

In local testing I make changes to our MySQL config file that is copied via the dockerfile:

COPY custom.cnf /etc/mysql/conf.d/

If I rebuild the containers locally my config changes are applied and the new settings a visible in the Mysql variables. show variables like 'max_connections' however they are not being set when the circle ci job is running the tests causing failures.

I am guessing some caching is being done (docker layer caching is NOT enabled in the config.yaml) how can I get the job to use the new configuration?

I am checking the config settings in MySQL and outputting the results during test and confirmed the old variable values are still being used.