When you use the mapreduce runner for the functional tests, it takes the ACCUMULO_HOME out of hte current environment and passes that on to the child test tasks.
Similarly, it should be taking ACCUMULO_CONF_DIR out of the current environment. Instead, right now it doesn't do anything for this value. Presuming the MR configs don't define it, this causes it to default to ACCUMULO_HOME/conf.
Workaround: define ACCUMULO_CONF_DIR in your mapred.child.env or modify config files in place within ACCUMULO_HOME/conf