Symptoms

There are duplicate tables in the MySQL Bamboo database some of which have names with all capital letters and there are ones with the same name but with small letters. This happens after restoring a Bamboo DB dump and running Bamboo. There might be errors stating that Bamboo cannot access some resources. For instance:

org.acegisecurity.acls.NotFoundException: Could not find ACL

Cause

MySQL case sensitivity with 'lower_case_table_names' variable is the culprit. The restored Bamboo DB dump contains tables with only lower case letters, and Bamboo adds some of the duplicate tables with upper case letters (after starting the Bamboo instance).

Resolution

1. Make sure that Bamboo database has been created by following the requirements. 
2. Run 'show variables;' in your MySQL to see the value of 'lower_case_table_names' variable. If it is set to 0, then shut down your Bamboo server and stop your MySQL DB system, set 'lower_case_table_names' variable to 1 by adding "lower_case_table_names=1" to the [mysqld] section of /etc/mysql/my.cnf file (for more info check this page).
3. Start your MySQL DB system, drop the Bamboo DB (as it got corrupted and contains duplicate tables), restore a correct Bamboo DB backup and run Bamboo instance.