Did you enter the mapper at some time, or not at all? The latter case would be really strange because I don't think the mapper file is written to at any other place.

Yes, probably so, though I can't remember what I was trying to accomplish at the time. Would it be possible that the change to the mapper file is originating from setting joysticktype=none for a particular game, and then simply opening and saving the mapper settings (thus without changing anything in the mapping)?

Would it be possible that the change to the mapper file is originating from setting joysticktype=none for a particular game

I think the idea was that this wouldn't change any mappings. The main focus was on what happens when you
have one joystick attached (4axis) then add a second one (2x 2axis) and whatever combinations that gives
with forcing one or the other.

The aforementioned issue only occurs whenever a mapper file is loaded/active that contains full joystick mappings (as show in the first post in the first blockquote) but no actual joystick is detected upon DOSBox startup (I simply unplugged mine). Then, when saving the mapper data, the joystick section ends up being overwritten into something similar to the second blockquote above.

The strange thing is that when starting DOSBox without an existing mapper file, and without a joystick, one can save the mapper data to file and the correct joystick section is saved (full mappings).

Is this a bug?

I was writing about it many times and that is why I introduced following line to manual:

"It is important to remember that if you saved the mapperfile without joystick connected, or with a different joystick setting, your new setting will not work properly, or not work at all, until you reset DOSBox's mapperfile."

http://www.dosbox.com/DOSBoxManual.html#Joystick