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This bug still exists in ESXi/vCenter 5. Opened a case, #12177367605.
/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/newVM1 # vmware -l
VMware ESXi 5.0.0 GA
/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/newVM1 # pwd
/vmfs/volumes/Shared/newVM1
/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/newVM1 # ls -lh
-rw------- 1 root root 2.0G May 23 12:08 newVM1-flat.vmdk
-rw------- 1 root root 8.5k May 23 12:08 newVM1.nvram
-rw------- 1 root root 514 May 23 12:09 newVM1.vmdk
-rw-r--r-- 1 root root 0 May 23 12:09 newVM1.vmsd
-rwxr-xr-x 1 root root 2.7k May 23 12:09 newVM1.vmx
-rw-r--r-- 1 root root 261 May 23 12:09 newVM1.vmxf
/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/newVM1 # ls ../templateVM1/ -lh
-rw------- 1 root root 2.0G May 23 12:01 templateVM1-flat.vmdk
-rw------- 1 root root 8.5k May 23 12:01 templateVM1.nvram
-rw------- 1 root root 496 May 23 12:09 templateVM1.vmdk
-rw-r--r-- 1 root root 0 May 23 11:42 templateVM1.vmsd
-rwxr-xr-x 1 root root 2.8k May 23 12:01 templateVM1.vmtx
-rw-r--r-- 1 root root 266 May 23 11:42 templateVM1.vmxf
-rw-r--r-- 1 root root 121.6k May 23 12:01 vmware.log
/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/newVM1 # cat newVM1.vmx | grep -i vmdk
scsi0:0.fileName = "/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/templateVM1/templateVM1.vmdk"
/vmfs/volumes/4eb18412-e8f5bca4-1d84-0050562e0c88/newVM1 # cat ../templateVM1/templateVM1.vmtx | grep -i vmdk
scsi0:0.fileName = "templateVM1.vmdk"
