So if you let OSMC run for an hour, note down the total system uptime, reboot, then check the total system uptime again it is less than before you rebooted ?
What happens if you run the following command via SSH and let it sit for a while ?
watch -n 1 grep systemtotaluptime /home/osmc/.kodi/userdata/guisettings.xml
This will monitor the systemtotaluptime value saved in guisettings.xml, which I believe is in minutes.
Does the number change if you use quit/exit ?