Is that a built game you're showing? Your setup should look similar to this:
[GAMERUN]
realgameview=0
dynamiclighting=1
dynamicshadows=1
useeffects=1
useeffectsonguns=1
useeffectsonscene=1
useeffectsonentities=1
useeffectsonessentials=1
dividetexturesize=0
optimizemode=1
hsrmode=0
[GAMEMULTIPLAYER]
multiplayergame=0
gameobjectivetype=0
gameobjectivevalue=0
oneshotkills=0
maxplayers=0
spawnrandom=0
[GAMEMAKE]
lightmapping=1
lightmapsize=16
lightmapquality=20
lightmapshadows=1
[GAMEDEBUG]
exitpromptreport=0
debugreport=0
showentitygameinfo=0
showdebugtextingame=0
debugreportstepthrough=0
usesky=1
usefloor=0
useenvsounds=1
useweapons=1
includeonlyvideo=0
includeonlyname=gamecore
width=1024
height=768
depth=32
useuniquelynamedentities=0
[GAMEPROFILE]
key1 = 17
key2 = 31
key3 = 30
key4 = 32
key5 = 57
key6 = 46
key7 = 13
key8 = 19
key9 = 16
key10 = 18
key11 = 42
global = languagebank\english\gamebank\mygame\setuplevel.fpi
levelfpm1 =
levelfpi1 = languagebank\english\gamebank\mygame\loadingpage.fpi
Wait... you're using Mystic Mod, I presume? Then I wouldn't know why it changes the setup file from its original state.