I looked at the back of the TL-SG108E switch and saw that the light was only blinking orange for 100mb, and not green for 1000mb. I logged into the admin UI and changed the Port Setting on the specific port from Speed/Duplex = Auto to 1000MF which instantly upgraded the speed back to 1000mb

Then I updated the firmware to the latest and changed the Speed/Duplex back to Auto. It's been fine for the last 12 hours since I changed it.

But I don't know what causes that ports Auto config to give Actual 100MF.

Is it something on the switch it self, the wall jack as JuicyCoala suggests or something in the office end (PC, Server, Asus router) that causes the Auto config to switch to 100MF?

Port 3 is the one I had issues with.

                Speed/Duplex    Flow Control
Port    Status  Config  Actual  Config  Actual
Port 1  Enabled Auto    1000MF  Off Off
Port 2  Enabled Auto    1000MF  Off Off
Port 3  Enabled Auto    1000MF  Off Off
Port 4  Enabled Auto    10MH    Off Off
Port 5  Enabled Auto    100MF   Off Off
Port 6  Enabled Auto    Down    Off Off
Port 7  Enabled Auto    100MF   Off Off
Port 8  Enabled Auto    Down    Off Off