I've configured Ethernet ports 11-13 on my RB1100AHx4 to be WAN ports. Initially they linked at 1G. I unplugged the ethernet cables to test the activity and loading on each service but when reinserted the port only connected at 100M.

I've rebooted the router, removed and reinserted the ethernet cables and power cycled the router but it refuses to connect at 1G. The settings say the ports are set to Auto with speeds to connect up to 1G (default settings). In winbox under Interface/ ether11/ Status it says the partner is advertising 1G but ether11 is only advertising 100M.

How do you reset it given the settings say it should be advertising 1G?

ROS v6.38.5

Did you try to force 1G instead of auto neg?

Also did you try another cable or another remote device?

You can select what rates it will advertise in the Ethernet tab of the interface. But if you get less that expected with auto neg it's most likely a cable issue or a non-compatible auto neg remote device. Usually forcing the rate on both ends fixes this.

I've found that forcing rates is almost always a bad idea, and should only be a used to lower the rate, never raise.
If you are not getting a 1G link, there is a reason for it. Something is wrong. Step 1 would be to use a network cable tester.
(not the cheap kind that just lights up)

Usual causes are:
1) defective cable - crushed, bent too far, twisted too tight
2) defective RJ45 - pins not seated correctly, oxidation
3) poor cable routing - running a long ethernet parallel with power, next to light fixtures, near high voltage
4) failing interface - One device or the other could be starting to fail.

Using a Fluke cable tester would be able to check all of those and give you a report of the most likely cause.

I've used replacement cables, even though it was working correctly just prior to unplugging and reinserting that triggered the incident. I've tried different devices - RB450G shows the RB1100AHx4 isn't advertising 1G. Also a TG789vac V2 modem also doesn't connect at 1G that previously did.

WEBFIG status of ethernet port Winbox ether port setting ROS v6.38.5
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I've configured Ethernet ports 11-13 on my RB1100AHx4 to be WAN ports. Initially they linked at 1G. I unplugged the ethernet cables to test the activity and loading on each service but when reinserted the port only connected at 100M.
ROS v6.38.5

I powered down and removed ethernet cables from port 11, 13. I then waited for the router to boot. After checking the router was fully functional in WEBFIG I reinserted the WAN ethernet cables. Ether13 resumed at 1G once more. Ether11 only linked at 100M.

Very interesting. You should do a supout.rif and email it to support@mikrotik.com. I think you may have found a bug.

Very interesting. I think you may have found a bug.

Issue and supout.rif submitted.

Very interesting. I think you may have found a bug.

Issue and supout.rif submitted.

Updated to latest stable release v6.38.7 but no change.
Support seemed confused asking me to enable "1000M-full" which can be seen in the image above and that I also provided.
Another observation is ether11 negotiates the link much slower than ether13.

There is no bug here. Your Webfig and Winbox are opened at different location, different menus.
Webfig shows interface status.
Winbox shows the settings you can set.

The question why your interface is linked at 100Mbit is different, cable, other device etc.

The problem is the setting is to advertise up to "1000M full". Both the RB1100AHx4 and connected devises only see an advertised speed up to 100M. Winbox status also shows only 100M advertised speed (not shown in these images). The connection actually connects at 100M, why? Cables checked (1m long), changed and alternate devises tried.

It appears the 1m short cable that worked in the beginning with the RB1100Ax4 and with other devices is the issue. It tests good with a Pockethernet tester https://www.pockethernet.com/. I don't have any other cables of the exact length so a 2m cable is in use.

Thankyou Normis. It appears that internal settings and the UI got out of step. The Netinstall brought it all back in sync, operating and displaying the same thing.