I ran into an issue recently where I could not do a GRT (file & folder) based restore from a backup that had been created using the VMWare Agent. The backups all reported as successful and I confirmed the GRT settings were configured in the backup options correctly. I also confirmed that the Remote Agent was deployed on the virtual machine and communicating correctly.
Basically, when I selected the virtual machine in Backup Exec 2012 (because you do a GRT based restore through the Remote Agent) the restore wizard only had the option for a full virtual machine restore. There were no other options in the restore wizard. I could only restore the entire virtual machine and all its virtual disks.
Apparently this is a known issue but there is a very simple workaround. To be able to do a GRT based restore from a backup using the VMWare agent I had to first do a one-time backup through the remote agent, treating the virtual machine as if it were a physical box. It didn’t need to be much. In fact, I just backed up one, yes just one, tiny little file through the remote agent. It didn’t even matter what destination I used. Once the backup completed I went back into the restore wizard and Hey! Presto; I now had an option to restore files and folders. Furthermore, it showed every single file and folder from the full virtual machine VMDK backup.
(At the time of writing there is currently no hotfix.)