Hi Hrobocop, i recomend in your auto-update script add delay between load new firmware and reboot.
:log info ("Downloading new RouterOS on router $[/system identity get name] from $[/system package update get installed-version] to $[/system package update get latest-version] (channel:$[/system package update get channel])")
## Wait for mail to be send & download FW
## Wait for upgrade all mikrotik in network, then reboot
:log info ("Upgrading RouterOS on router.")
In my net i have many Mikrotik devices, when it "all" start update at same time, on some one devices downloading has fail, because uplink(up Mikrotik) has rebooted first.
Also i add to begin
/system backup save name=disk1/before_firmware_update
Because some times Mikrotik has died on update.