Aligned VMDK failed to backup with the Netvault Vmware plugin (4046090)

Some users will use third party tool like netapp MBR alignment to align their VM vmdk to improve performance of the machine. After the vmdk alignment normal day to day operations work fine on the VM. However the backup of the VM fails.

Binary log message will report the failure as follow

Job Message 2012/03/12 11:20:34 3500 Data Plugin LDNNETVAULT1 Determining VM disk areas to backup
Information 2012/03/12 11:20:34 3500 Data Plugin LDNNETVAULT1 All sectors on disk '[ILIOStore] VDI-XP-ProdSupp/VDI-XP-ProdSupp-000011.vmdk' will be backed up
Error 2012/03/12 11:20:36 3500 Jobs LDNNETVAULT1 Job manager lost message channel unexpectedly

We have found that vmdk size as obtained from the snapshot is always zero after the alignement.