This has only happened to me with the variables file so far. I don't know if it's an issue with the control.ini file. And I thought I heard about a fix done for this issue, but just in case...
Do you manually edit the control file while mirc is running? I noticed this same behavior happening with my variables. I would restart mirc and the changes I had made were gone. I checked the actual file and I saw two [variables] sections in the file. mIRC would only read the 1st one on startup. It would happen when I manually edited the file while mirc was running.
