Sounds like somebody changed the filing policy on your devices.
In CWIS go to Address Book and select one of the FTP addresses and choose Edit
Image may be NSFW.
Clik here to view.
Then check that the Filing Policy is set to Change Name and that the Folder options are as seen here as well.
Image may be NSFW.
Clik here to view.
If this is not the correct answer to your issue, please provide the full details of how the scan is setup and I will see what I can figure out.