You probably run with more than 60fps, this can make cate move real slow (especially when crouching). You can limit fps ingame by going into Options -> Experimental Settings and set 'Unlock Framerate' to 'No'
Make sure that both Nolf2.exe and Lithtech.exe runs with administrator privileges, settings will not be saved otherwise.
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To run the game without the launcher, pass all needed arguments directly to lithtech.exe:
lithtech.exe -windowtitle "No One Lives Forever 2" -rez Custom\Resources\Nolf2_custom_jan_19.REZ -rez GAME.rez -rez GAME2.rez -rez GAMEdll.rez -rez Sound.rez -rez GAMEl.rez -rez custom -rez GAMEp.rez -rez GAMEp2.rez -rez MapPack001.rez -rez MapPack002.rez -rez Update_v1x3.rez -rez Custom\Mods\Modernizer\Modernizer.REZ
You can also add settings to this string such as:
+DisableMusic 1
You'll find the full string stored by the launcher in launchcmds.txt