Every time you enter a command into your autoexec.cfg or into the console, it registers a permanent change into your "master config". Unfortunately, the way that configs work in ET are kind of confusing, and there isn't really one "master config" file! In fact, there are several config files and to make matters worse, all those files have the same name! (They're just in different directories).

Here are some of the config files I have:

C:\Program files\Wolfenstein - Enemy Territory\etmain\etconfig.cfg
C:\Program files\Wolfenstein - Enemy Territory\etmain\profiles\Raj\etconfig.cfg
C:\Program files\Wolfenstein - Enemy Territory\etpro\profiles\Raj\etconfig.cfg
C:\Program files\Wolfenstein - Enemy Territory\shrubet\profiles\Raj\etconfig.cfg

The first one, in the "etmain" directory is not really ever used. It's simply a backup copy of the original config, and contains all the default settings. So, if you ever mess up your config, what you can do is copy lines from this backup config into your "active" config files-- basically every "etconfig.cfg" except the backup one is an "active" config file.

The next config file on the list is in "etmain\profiles\Raj\". That config basically stores whatever changes you make on the options menu.

The last couple of config files hold whatever settings you change during an actual game. They are in the "etpro" and "shrubet" folders. Etpro and shrubet are two of the most popular variations of ET. Depending on what server you play on, the mod of ET it's running might be different. In that case, you might have additional directories. You can find out what type of game a server is running by going to the options menu and clicking on "Server Info".

Each mod acts like a whole new game. When you connect to a server running a particular mod, that mod (and therefore that config file) are applied. This also happens when you manually start a mod from the mods menu.

So, say you're on a shrubet server, and you go to the console and say "/set name Bob". Then, when you play on a shrub server, your name will be Bob. However, when you play on something else, you will have some other name, because it uses a different config file for each kind of ET modification!

Obviously this can get really confusing having all these config files. Especially for things like your name, you don't want that changing depending on what mod the server you're playing on is running! So, what I'd recommend is store important settings like your name in your autoexec.cfg (use "set name ...."), and then just create a key bind for "exec autoexec.cfg". Then when you join a server, you can just run your autoexec and be done with it.

So, how does ET decide which config file to run at which time? There are so many of them! Well, when you start up the game, the config file at "\etmain\profiles\Raj\" is applied. Immediately after that, your autoexec.cfg is applied. Then when you join a server (say it's a server running the etpro mod), then the mod-specific config file is applied (like the one for shrubet or etpro). So as you can see it's really a messy process - that's why I recommend just sticking all the important stuff in autoexec and having a keybind to easily execute your autoexec after you join a game.