That doesn't "fix" anything, unfortunately, because nothing is broken. Let me explain.
In order to facilitate map rotations across changes in gametype I implemented a system whereby the game executes one of four .cfg files depending on gametype. Any time the g_gametype cvar is changed it will execute the new config so yes, the first map will always be the first one in the rotation no matter what. However, once that map loads you CAN select any map and it will load that map properly.
The reason I went to this system was twofold. First, it fixes the lack of map rotation problem when you change gametypes. It's awful when people want to play CTF or Team DM and callvote the gametype change and you're stuck on FFA maps. Can't play CTF without flags! Second, I did not have time prior to .99e's release to do what I want to do with the map rotations and switch over to a list-style format in the code.
In the upcoming bugfix patch this new rotation format will be implemented, and those .cfg's will be replaced with a new list-style format. These files willl still autoexec, but it will not automatically force the first map in the list. They'll be held in a que. Servers will also gain the ability to randomize the map rotation to keep things interesting.
In the mean time, if you want to change the files I'd recommend changing the last line in the file to "set nextmap vstr m1" instead of wiping them clean like that. Then you can load any map you want from the getgo and still have some kind of map rotation present.
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