some times you will find the master in a hbase cluster cannot be stopped, so check the following two items suggested by some guy in hbase user mail list.
But I'm not sure it helps.
> If zookeeper is not running (or do not have the quorum) in a cluster setup, hbase does not go down..bring up zookeeper
-> Make sure pid file is not under /tmp...somtimes files get cleaned out of tmp..Change *env.sh to point to diff dir.