My scheduled scan also reverts to "Disable", going back as far as I can remember with this router. I'm using ext4 on my drive.
Some problem here on RT-N16.
Starting a Restart Scan on Disk Utility, my Generic Flash Disk is unmounted and then scanned, but still freezed at 90% remounting disk and the USB icon become red.
Starting e2fsck from shell the file system (ext3) is correct.
Same problem reported by tommyv2 with scheduled scans, always revert to "Disable".