It looked good when I created it (plain text editor), It looked good when I previewed it, it looks like crap now it is posted.  So here is a properly formatted version using the 'pretty' editor

Master Windows Server 2012, Netbackup 7.6.0.1
Clients, Windows Server 2008 R2, Netbackup 7.6.0.0
Storage Unit, EMC Data Domain via Basic Client
The account that the services (NetBackup Client Service, NetBackup Remote Manager, NetBackup Service Layer) run under has administrative rights to all file areas. All other services run under system credentials

Background:
Numerous off site servers use DFS to replicate there data back to my site for backup
I can browse all of the replicated data on the 'centralized' server
If I choose Select files for restore I can only see the topmost folders*

*If I create a folder, drag and drop the exact same files and or copy them via the command line, they are available for individual restore

How are your policies configured? Sounds like you may be missing a setting / configuration within there. 

? The backups are running and reporting files and sizes that would indicate the backups are being made, I am running a test tonight. I am going to first verify I can only see the topmost folders of some disposable data then whack and restore it. I just don't want to have to restore 40GB of data to get one 5MB file.

I can not find anything on the Windows side that would cause my ability to see the files to go away on the netbackup side. I am not an administrator of the EMC box and 'they' don't support Netbackup.

Can you doublecheck your configuration if you're backing up Windows DFSR?

Backup and Restore of Microsoft DFSR data using Symantec NetBackup

Battling to understand where you are creating the folder that makes the files visible for restores?

Or maybe doing another backup after copying the files into the new folder?

The BAR GUI will show what was backed up.

If we know what your policy looks like and can see a screenshot of BAR GUI, we may get a better understanding of your issue.

Policy config:

bppllist <policy-name> -U

Thanks for the command line, it ended much head scratching. I will be creating a duplicate policy with a fraction of the data to work with. 

Policy Name:       dfs01-e-drive

  Policy Type:         MS-Windows
  Active:              yes
  Effective date:      02/20/2015 16:37:59
  Backup network drvs: no
  Collect TIR info:    no
  Mult. Data Streams:  no
  Client Encrypt:      no
  Checkpoint:          no
  Policy Priority:     0
  Max Jobs/Policy:     Unlimited
  Disaster Recovery:   0
  Collect BMR info:    no
  Residence:           EMC-DD
  Volume Pool:         NetBackup
  Server Group:        *ANY*
  Keyword:             (none specified)
  Data Classification:       -
  Residence is Storage Lifecycle Policy:    no
  Application Discovery:      no
  Discovery Lifetime:      28800 seconds
  ASC Application and attributes: (none defined)

  Granular Restore Info:  yes
  Ignore Client Direct:  no
  Enable Metadata Indexing:  no
  Index server name:  NULL
  Use Accelerator:  no
  Optimized Backup:  no
  HW/OS/Client:  Windows-x64   Windows2008   scfmfdfs01

  Include:  E:\

  Schedule:              Full
    Type:                Full Backup
    Frequency:           every 7 days
     Excluded Dates----------
        No specific exclude dates entered
        No exclude days of week entered
    Synthetic:           0
    Checksum Change Detection: 0
    PFI Recovery:        0
    Maximum MPX:         1
    Retention Level:     3 (1 month)
    Number Copies:       1
    Fail on Error:       0
    Residence:           (specific storage unit not required)
    Volume Pool:         (same as policy volume pool)
    Server Group:        (same as specified for policy)
    Residence is Storage Lifecycle Policy:         0
    Schedule indexing:   0
    Daily Windows:
          Friday     17:00:00  -->  Monday     07:00:00

  Schedule:              Differential-Inc
    Type:                Differential Incremental Backup
    Frequency:           every 1 day
     Excluded Dates----------
        No specific exclude dates entered
        No exclude days of week entered
    PFI Recovery:        0
    Maximum MPX:         1
    Retention Level:     1 (2 weeks)
    Number Copies:       1
    Fail on Error:       0
    Residence:           (specific storage unit not required)
    Volume Pool:         (same as policy volume pool)
    Server Group:        (same as specified for policy)
    Residence is Storage Lifecycle Policy:         0
    Schedule indexing:   0
    Daily Windows:
          Monday     17:00:00  -->  Tuesday    07:00:00
          Tuesday    17:00:00  -->  Wednesday  07:00:00
          Wednesday  17:00:00  -->  Thursday   07:00:00
          Thursday   17:00:00  -->  Friday     07:00:00

So, policy backs up E-drive.

Are there any mount points under E:\?
(NBU does not cross mount points by default.)

Is E:\ or any folder under E controlled by DFS-R?
(DFS-R folders are filtered into Shadow Copy Components.)

Does the logon account for NBU Client Service have sufficient permissions to read/access all folders under E:\?

When you browse for restores, the image catalog is browsed on the master server, not the DD.

So, we first of all need to confirm that E:\ and all of its subfolders are getting backed up.

To see what is happening on the client during the backup, ensure bpbkar folder exists under ...\netbackup\logs on the client. 
Increase Client logging level to 1.
After next backup, you will see a record of each file and folder that is getting backed up in bpbkar log.
Reasons for anything being skipped will also be logged.

If you need assistance with reading bpbkar log, copy to bpbkar.txt and upload as File attachment.

Sorry for the long delay, there is only one of me, and thousands of 'them'.

Are there any mount points under E:\? No

Is E:\ or any folder under E controlled by DFS-R DFS, Yes, DFS, those are the folders that I can only see the topmost level of.

DFS-R folders are filtered into Shadow Copy Components ? I must be thick or it changed between Server 2003 R2 and 2008 R2. The exact same data on older servers running identical versions of NetBackup show all of the files, replicated or not. I did a couple hours of testing with screen shots just to prove to my boss I am not crazy.

Does the logon account for NBU Client Service have sufficient permissions to read/access all folders under E:\? Good question, the account on the DD is not a Domain account but an account that is local to the DD but shares a name and password value. Changing the password on the Domain does not change the password on the DD so I know they are not magically linked. The AD account is in the server administrators account. There is an account by the same name on the DD. All of my writes to the DD failed until I changed the 3 services so they ran under the user that is mirrored on the DD. That is thanks to someone else who is also here :) 

When you browse for restores, the image catalog is browsed on the master server, not the DD. Correct, I do not/can  not do anything directly on the DD

I am off to follow the other steps you have given me. I did a not so quick test that appears to show the files get backed up until their are added to a replication group. Like I said previously, historically this made no difference. Or I just got lucky...

Thanks, I read it! The log you had me generate mentions filtering shadow copy components. I'll upload the log as soon as I figure out how. My biggest question will be how I was able to back up the replicated data for all these years as files with out taking any additional steps. I don't recall having a vendor come in.