Are you accidentally doing remote agent backups? (In other words backing up the virtual server as if it was a physical server.) If you are then the backup selections will not show the VMDK files as these are part of selecting via the VMware server (Vcenter or ESX Host)
Do you mean vmdk files are not visible in the restore selections after the backup? If you do, are you aware that you see vmdk files by selecting the restore from the VMware object (VCenter or ESX Host) but you see the GRT data by starting the restore from the hostname or DNS name of the virtual machien itself - as such are you looking in the correct place?
