Go back to your saved scene ( !important). Now turn on hidden geometry (view menu) and those hidden groups will show up. Now you can right click and unhide them. Now click on your scene tab and "update" it.

The only other thing I can think of that might cause this, may be Firmware write-cache handling by the IDE of the harddrives themselves.

To change this you would need to run an OEM utility downloaded from the harddrive manufacturer's website.