If Region server checkin after call this.serverManager.waitForRegionServers(). It seems that regionServerReport shouldn't add Region server to onlineServers. Otherwise The region may be opened again.
In my cluster: 2011-05-23 10:56:30,726 INFO org.apache.hadoop.hbase.master.HMaster: Master startup proceeding: cluster startup 2011-05-23 10:56:30,726 DEBUG org.apache.hadoop.hbase.zookeeper.ZKAssign: master:20000-0x2301a9c63bd0006-0x2301a9c63bd0006-0x2301a9c63bd0006 Deleting any existing unassigned nodes // Region server register later , So the 1344 regions had opened in other region server. So, I think it should shutdown machine 158-1-101-82. 2011-05-23 10:56:33,504 INFO org.apache.hadoop.hbase.master.ServerManager: Registerring server=158-1-101-82,20020,1306117051387, regionCount=1344, userLoad=true 2011-05-23 10:56:33,875 INFO org.apache.hadoop.hbase.master.AssignmentManager: Bulk assigning 5041 region(s) across 1 server(s), retainAssignment=true 2011-05-23 10:56:33,876 DEBUG org.apache.hadoop.hbase.master.AssignmentManager: Timeout-on-RIT=5041000 2011-05-23 10:56:33,876 DEBUG org.apache.hadoop.hbase.master.AssignmentManager: Bulk assigning 5041 region(s) to 158-1-101-222,20020,1306119315097
