I have my own UT3 server that can't be added to GT...
It's running, I can join using connect by IP, but it doesn't show up in the UT3 GameServerBrowser MasterList (does that matter?).
I've forwarded my the ports necessary, disabled my firewalls, tried to whitelist the given ip's in error message on GT and added queryport 6500 in command as I didn't do that before, just to make sure it is correct. What can be the problem and how can I solve this?

You seem to have everything you need setup. What is the IP port and Query port?

My ip of server is 84.85.81.75, port:7777 query:6500
I added query in command line, don't know if it's set anywhere else that may override it?

Are you hosting this from home? Does your ISP have anything in place to be blocking you from hosting things like this?

Yes, I host this on my own Gaming Pc at home. As far as I know my ISP doesn't block it, but I'm not sure either. If there is nothing else to try, then I have to ask them. In case they do block something, what can it be and what do they need to change?

You tell them that you are 100% sure everything is open on your end (if you are sure) but external users cannot join your server. Essentially if you look above you should have the information you need.

I've finally tested it today and external players are still able to join my server. I changed it because it failed a few days ago. Now the NAT is open for first time (instead of moderate that worked before) but I've never had the chance to check if it works. Now I'm sure people can still join it. Everything is open, forwarded and disabled as far as I needed. It doesn't show up in the serverbrowserlist of UT3, but it's not the case that GameTracker only looks for servers in that list?
I don't know what to do to make it visible there and what can be the problem of adding it here on GameTracker...

GameTracker does not scan any master server lists for servers.

My only other suggestion would be to check if your IP is still what was previously mentioned. Most ISPs give residential customers dynamic IPs, meaning it may have changed on you.

My IP never changed since we moved to that ISP.
And as people can join it, the IP is correct and that's the one I enter in the box for server ip.
My server is not offline, of that I'm sure.
I disabled my Windows FireWall and have no other ones installed, so any blocking shouldn't be possible in this case? (unless ISP does?)
And the query port is setup in the command line, but there's nothing that overrides it somewhere? How can I check that port after I actually ran the server? It's my only lead, as I can only verify I set it, but I can't proof it uses that port anyways...

7777 and 6500 are the defaults from my understanding for UT3.

You can try downloading HLSW and see if you can scan your server locally by entering the address in the form of 84.85.81.75:7777:6500. That will help you determine if it is likely a configuration or mod issue (cannot scan it) or a port issue (you can scan it locally).

This is about all the help I can be. Assuming you've done everything correctly that you said you have done, you should be good to go.