Caddy HDD files is now partially visible.

My computer is using windows 8.1.1. as part of my backup procedure, I installed the latest Macrum reflect update,
then restart as requested. During the restart the Avast! updated without my permission. During restart I observed there the Windows update notification (both right of login screen) disappeared. After restart, I plug-in my backup caddy and discovered I could see on one file from previous backup but no other file were observable (expecting 1000s). Serious, I cannot see my backup files! I have done the following investigation so far:
- Reboot windows mutliple time ... no change
- Confirmed no windows updates were perform during restart
- Disabled Avast!, but does not make HDD files visible
- Check caddy diskspace uage, it reports 280GB of 300Gb used.
- The full contents of the caddy can be view in XP.
- Confirmed Caddy driver is up-to-date
- Change to full access for all users names in the drive. Observed it was processing the invisible files! No change to the file visibilityafter processing

I suspect a windows problem at this time. Any idea what causing partial visibility of a Caddy HDD contents and fix it?

Discovered the cause of the missing directory. The E:\backup\data directory have been assigned hidden system proproerties. Found "attrib -A -H -S E:\backup\data" command was able to remove these unwanted properties.

Since I don't know how to assign system/hidden properties a directory/file, so I'm unclear how or what made this directory a hidden system file. Is there a way to force Windows to prevent system/hidden permissions being assign
to any file/directory outside of C drive?