As the topic says, just wanted to write this up in case it helps anyone else, as it took me a while to figure this one out, and I was almost going to return the unit.

My first MikroTik router (coming from Edgerouter Lite) - an RB5009UPr+S+ (the POE model) - the symptoms:

ethernet port 2 would not work like the other ethernet ports if you plugged a cable into it. Symptoms:
- Two Ubiquiti POE switches would not come up with a link at all, no matter what cable or what port on the Ubiquiti switch
- Two USB - Ethernet 1Gpbs dongles would eventually (5 seconds) show a link, but only 100Mbps Full Duplex, not 1Gpbs
- Looking in winbox, the port status said when the USB dongles were connected that the other side did not offer 1Gpbs, only up to 100Mpbs
- Poe Status was "Short Detected"

If you plugged the Ubiquiti or the USB ethernet dongles into any other port on the RB5009, they'd come up in 1Gpbs F/D straight away, and POE would go into "Waiting for load" - it was only that ether2 port. I tried loads of cables, made no difference. And yes, port settings were the same for all ether ports (only different one is ether1 as that is 2.5 Gpbs). Playing with auto negotiation made no difference either.

So it had to be an issue with ether2 specifically, and it seemed broken. Had tried blowing out the port and gently cleaning contacts with alcohol, didn't help (was a new unit anyway, didn't expect dirty contacts but you never know).

Was about to return the unit under warranty when someone pointed out that (apparently) 1Gpbs and up use wire pairs that lower speeds do not, so to only have 1Gpbs fail suggests that one of those contacts may be the issue. And the POE did moan about Short Circuit, right?

So, I had one final good look at the pins using a magnifying glass - and that's when I saw it:

The contact pins in the RB5009 ethernet sockets come up from below in the socket at the front and are then bent backwards, forming a contact rail running towards the rear of the socket. To stop them touching, they run in little plastic guides, with ridges either side of a pin to stop two pins touching. At the rear, these ridges don't run all the way to the top and they are "open" at the top.

The leftmost pin had jumped from its guide and had ended up in the guide for the pin to the right of it, making them touch at the very back. The solution was to use a small hook tool to lift that pin up until it cleared the guide, move it to the left and push it back down in its correct position. After that, the port worked fine again. Phew!

I checked with at least one other device, in the sockets for that device there is a little plastic "bar" at the back running horizontally across the guides, so a contact pin can't "jump" its guide. On the RB5009 sockets, there appears not to be such a bar and the guides don't run all the way to the top. So it seems pins can jump, causing a short and all sorts of weirdness.

Like I said, fixed for me and no harm done but I thought I'd write it up in case anyone else experiences similar weirdness on an ethernet port: it could be a shorted pin that jumped its position.