Forgot to mention. Doing a speedtest speeds start off at 900 and then quickly drop to the final 500.

  @Sunshine It turns out the following is happening:

Ports 1 and 2 are full speed and I haven't seen a drop on these.

Port 4 mostly is at full speed but sometimes there is a drop.

I didn't check port 3

Ports 7 and 8 would mostly not even negotiate and when they did the upload speed was always 100Mbps. Even if I then swapped from 8 to 2 and back again, for example, 2 was always 900Mbps upload but 7/8 was 100Mbps. 

I didn't check ports 5 and 6

I couldn't work out how to connect the laptop directly to the ONT due to VLan id settings required by my ISP. However, given the tests above it seems some are negotiating at expected speeds, 4 is weird and I'm putting that down to "other factors". I suspect 5 to 8 are all the same and negotiation is always 1000Mbps down but only 100Mbps up for some reason. Certainly 7 and 8 do this. That's when they negotiate. More often than not they reported no connection.

This was with QOS -> Standard. I forgot to try QOS off though it is now and port 1 is still working as expected.

Regards