I found that minew weren't being logged until I closed mIRC (actually, I hadn't planned on closing it, there was a power failure, so my system shut down.., LOL )
These settings do overwrite the mirc.ini file, because that is where they are stored, so if you're using a different mirc.ini file, then the settings wouldn't be stored.
Other than that, I'm afraid I'm out of ideas.
