[otrs] Problems making changes permanent

Hi there I have basically asked this question before, but haven't gotten an answer yet. I'm trying to change the system using SysConfig but so far just a few of the changes actually replicate throughout the system. I have tried to figure out where the changes are stored, since the "Reset button" still is there after a restart of the web server, and I've narrowed it down to the files ZZZAAuto.pm and ZZZAuto.pm in /usr/share/otrs/Kernel/Config/Files. Looks like all my changes are there, but I don't see how this file is in any way used by the system? Can anyone shed some light on this issue? Marius