MySQL innodb_log_file_size change is not being recognized
We tried the same procedure on an Ubuntu workstation with MySQL 5.7.x on Ubuntu 16.04 and it worked without issue. 

Based on this, we decided to upgrade our server's OS to Ubuntu 16.04 which upgraded MySQL to v5.7.12. After changing my.cnf to reflect changes in some option names and restarting the service, the log files now have the correct sizes and the problem is resolved.