@ I believe it does a hash check on the default .ini file and if it’s changed it will generate a new UDK .ini.
This means you need to be careful of when you even simply save your default .inis as it will reset your player’s settings to default.
Each time i add or make a change to the defaults this happens, but my players are quite forgiving about it. Try not to do it too often though. I usually arrange it so newly added vars default to false, so i don’t have to touch the default .ini.