Depends if you're using OpenJK or Jamp, I think one of the .cfg's is in documents --> my games
The other is somewhere in your gamedata
To backup just copy the .cfg with your settings in it and put it somewhere safe if it gets deleted again.
I dont think your PC is good enough to run the game at the settings you have it at.
Try putting all graphical settings to the lowest they can be.
Also switch to the MBII/OpenJK engine in Launcher --> settings (uncheck steam integration) switch from Jamp to MBII - this is more stable running...
You can increase your Geometric Detail, Texture Detail and Texture Quality
as well as set detailed shaders to 1
You should cap your fps to 125 or below
Make sure to set Enhanced Effects to normal
That's a very weak cpu Emmanuel, which might be the cause of some of your problems - graphical settings like you mentioned are affected by gpu performance, unlike showing many players at once which is more cpu-bound.
*edit* try setting enhanced effects to 'normal' down from 'high'
Butternut...
A lot of peneke models are not optimised to be part of the base game, they may result in a performance hit for ppl with worse pc's. They would need to be altered or re-created from the ground up