SELECT GET_LOCK() showing up in slow query log (CI SESSIONS)

You can just ignore this.

It's caused by the same user attempting to simultaneously load multiple pages (or one page with asynchronous AJAX calls) on your website. And it's exactly what is supposed to happen - wait for the lock to be freed (session closed on one page) before being able to acquire a lock for the second page load.

Concurrent users and the database engine are irrelevant. You didn't see this on MyISAM just because you didn't have a user with the same behavior during that temporary switch.