I have a new OmniTik, just out of the box. It was running v5.4 and the rear LEDs were correctly showing Ethernet link/activity.
I upgraded the unit to v5.7 and the LEDs did not light up any more, then I noticed this:
So I reconfigured the LEDs and they're flashingly back.
I then tried to do a reset-configuration and checked again
So for everyone who thought their LEDs aren't working, check the LEDs window to make sure they're assigned correctly.