Backed up files partially disappear after restore (Windows Server 2008 R2 - Windows Server Backup)

Dear all,
I am experiencing a problem with "Windows Server 2008 R2", using Windows Server Backup.
Here's my setup:
Server: RAID 5 Disk setup
Backup:
By using Windows Server Backup (within Windows Server 2008 R2), C: and D: were fully backed up, with "System State" and "Baremetal Recovery" options selected. Backup went okay without any errors.
Restore:
By using Windows Recovery Environment (booted from Windows Server DVD), C: and D: were fully restored to the original partitions with "System Recovery" option found within Windows RE (without re-formatting partitions during restore). Restore
went OK without any errors. Rebooted, and system has been running fine.
Problem:
After the restore, the system itself seems running OK; no BSOD, no crash, no visible errors.
However, our client insisted some files (around 6 to 7) which are related to the propriety software has "disappeared" right after System Recovery.
Question:
Since Windows Server Backup is using "Volume Shadow Copy" technology which enables "live backup" of the running system, is it possible that some files will disappear (=restore error) after
System Recovery?
I cannot really find any errors or warnings related to Windows Server Backup in the event log, through. No Windows-backup errors. No VSS errors, too.
Do anybody have experienced this kind of problem in the past? Any suggestion will be greatly appreciated.

Thank you for your reply, Ms. Mandy.
To make things clear, let me explain to you briefly:
1. The "missing data" was backed up with "full system backup".
2. After a system restore from the above backup image, as you mentioned, partitions has been overwritten with the partions' backup data in the Backup Data Set taken by Windows Server Backup. No error with backup. No error after restore, and reboot - system
has been running fine.
3. Although there was a report that the affected files(about 7 java exectables) were missing after the above restore operation, other aspect of system was running fine at the time of the report.
4. I have checked the original backup data set - and voila, there ARE files which seems to gone after restore.
5. When I used Windows Server Backup "on" Windows Server 2008 R2 normal environment (= NOT Recovery environment from DVD) and selectd ONLY these affected files to restore, these files could be RESTORED successfully, without any errors. SO... data
was property backed up.
> The recovery will overwrite the partitions so files created after the backup point will be missing.
I understand, and this is not the case this time, because the affected files are already present in the backup data set (= I have mounted the backup data as VHD, and I could clearly see them present in the mounted VHD file)
Plus, these files are completely restoreable via "selective file restore" in Windows Server Backup.
Things I want to know/confirm:
> The recovery will overwrite the partitions
If I understand this correctly, in case that the files in question are already present in the backup data set, these files SHOULD be restored after full system restore, right? (If these files could not be restored, Windows Server Backup SHOULD show some errors.)
What do you think, Ms. Mandy? :)
Jo

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