You have enabled "Scan when a file is backed up," but you see no indication that Auto-Protect is scanning files during backup.
This is working as designed.
When you enable the option "Scan when a file is backed up," Auto-Protect only scans files during backup if any process is trying to write to that file. Normal backup operations only read the files it backs up.
When you disable this option, Auto-Protect scans no files during backup.
For Symantec Endpoint Protection 12.1.2, in the Symantec Endpoint Protection Manager, you can find "Scan when a file is backed up" in the Virus and Spyware Protection Policy, under Auto-Protect > Scan Details > Advanced Scanning Options. In the Symantec Endpoint Protection client, you can find this setting under Change Settings and then next to Virus and Spyware Protection click Configure...; on the Auto-Protect tab, click Advanced. This setting is found under Scan files when. However, if your administrator has locked down this setting in a managed environment, it appears greyed out and you cannot change it.
This setting may appear in different locations in earlier builds, but the behavior is the same.
The inline Help documentation inaccurately describes the expected behavior of the option "Scan when a file is backed up."