I set my flag file to have -master_data_dirs=/var/lib/kudu/master/ -master_wal_dir=/var/lib/kudu/master (note the lack of trailing slash on the WAL). In this case, the master fails to start up. If I change it so the trailing slash (or lack thereof) matches, then it starts OK. Note that this is on first start. Once it's initialized, it works fine even if it's inconsistent.