Virtual endorsement has precedence over the physical endorser. In order to ink an item you must turn on the endorser in GenericOptions.ini.
//GenericOptions.ini
[OptionalDevices]
NeedRearEndorser = true
You will also need to make sure virtual endorsement is disabled in RDMScanner.ini
//RDMScanner.ini
[VirtualEndorsement]
VirtualEndorsementMode = None