This is sorted out, according to support this is a bug. See below.
Thank you for reporting this problem. It is detected and will be fixed in
next RouterOS releases.
> Hi support,
> I've bought a brand new RB1200 router and configured it in a way where ports
> eth1,eth2 are routing traffic and disabled all other ports. All was working
> fine but a single system reboot command makes the router unusable any more
> as it passes no more traffic after this. The only way to make it work is to
> connect via serial console and enable all disabled ports (which were not
> used anyway) which is not a correct behavior.
> I've attached the supout file for your reference.