In a previous thread, one of the Activiti developers noted that the activiti-standalone-context.xml is no longer the file that should be utilized; I believe you have correct approach, using the 'activiti-custom-context.xml' file.
At a second pass of your log files, it looks as though there might be another problem - have you left the DemoDataGenerator active in your application? As the User Guide states, when attempting to integrate Activiti-Explorer with LDAP - you'll have to disable the demo data generation in order to stop the collisions that will happen.
And in your log files, I'm seeing:
So it looks like that is still be called somewhere in the tree, and could be the reason you're having some issues also.
Just a thought.