It is expected for the scan engine to revert to configuration mode after a reboot, even if you've set scan engine startup mode to be Active in the LabVIEW project settings. This happens because EtherCAT requires scan engine to be in Configuration mode
for it to cycle through various modes.
To change the scan engine mode, use Set Scan Engine Mode.vi
and Get Scan Engine Mode.vi
in your LabVIEW VI to explicitly place scan engine in the active mode.