After a little trail and error, I was able to find the locations of the entries that are messing up the gametype and mod menu of the latest version of U4E. I love playing the Gauntlet gametype, it truly does remind me of those good old days of me playing the original game in the arcades so long ago. Although I must admit, the original was never this much fun.
Here are the files to open and what to comment out in each of them. In case you don't know, you comment things out of unreal files by simply typing two forward slashes "//" before the line.
All of the files you need to edit are located in your UnrealTournament\System folder so open it up and do the following.
1) Open "gateway.int" in a text editor and comment out the line that starts with Preferences= so it looks like //Preferences=. Be sure to save your changes.
2) Open "U4eJailbreak.int" and comment out every line after the //add this to all game-object line. There are three lines that you will comment out of this file. Save changes and continue to the next file.
Optional) If you want to disable the normal UFE gametypes, by that I mean U4E Deathmatch, U4E Domination, etc. open "U4eT601.int and comment out every line in the file except for the very first line after the [Public] tag. All the unique gametypes like Gauntlet are kept in other files and it's real helpful disabling these "generic" gametypes when you have lots of mods installed. Assuming of course that you can easily play them just by using the mutator for the mod. In this case you can by using the U4E Tournament mutator in any of those normal gametypes.
I am pretty sure I listed the correct files and lines to comment out but just in case your version of U4E gets messed up, just remove the "//" you added to those files and you should be just fine. I have playing with them commented out for a while now and I have no problems but you never know.
If you are curious, here are the settings I like to use for the Gauntlet gametype. Some of the default settings were fine but I really did not like the defaults for the respawn rates and health of the portals. So here are the settings I have found over time that workes best for how I like to play.
Be sure to load a map that can support at least 12-16 or more players to make the game more interesting and to prevent the game from crashing. I tend to play with about 9 bots and with the U4E Night Of The Living Dead mutator. Things tend to get pretty hectic after a few minutes and you will really need the help when the bosses come onto the scene. Do not even think of playing this gametype on a small map unless you enjoy seeing UT crash.