I believe that the browse-start.bat "mounts" the desired VM under the C:\mnt (or whatever directory is specified in config.js), thus allowing the backup agent to backup the drive/file(s) from the VM.
The pre-backup.bat actually backs-up the full VM (as opposed to just creating the mount point).
I am not entirely sure of your question; I do know that the BackupExec VCB Interoperability Module documentation can be kind of difficult to follow (at least it was for me).
The most important thing I found is that for ANY sort of file-level backup to complete, you first HAVE to successfully perform/run the "C:\Program Files\VMware\VMware Consolidated Backup\backupexec\browse-start " to complete successfully.
The "browse-start.bat" command mounts the VMs' virtual disks under the C:\mnt\ (again, by default) of the VCB proxy, and you then browse to the files (on the VMs disk) as "Backup Selections", just as you would browse to any other file you are backing up.
If I am reading your question properly, it appears that the browse-start.bat is not completing successfully, therefore the VMs disk's are not being mounted underneath C:\mnt, and therefore you are not able to select these files to backup through the Backupexec GUI.
But, I may be misunderstanding your question/situation and you may already know all of the above.