The color settings (alt+b -> colors tab) seem to be in the mirc.ini under the cnicks section. Perhaps mIRC can't write to the ini file for some reason (read-only, full hdd, no permission, etc). Depending on how you run it, the settings might not even be in the mIRC folder. To find its location, you can type //echo -a $mircini. mIRC should automatically flush all settings to the ini file during a normal exit, but i believe that you can also use /saveini to update them manually. If it seems to lose those settings when you disconnect/reconnect, and not just when you reopen, it is possible that you have some odd commands in perform or in an on connect script, perhaps utilizing the /cnick command.
