1. I'm honestly not sure in which cases this color is applied...
2. If you modify mirc.ini while mIRC is running, mIRC keeps using the "cached" old values. And /saveini would write the cached values to the ini file, not vice versa. Afaik /flushini on mirc.ini has no effect. A /writeini plus /exit -nr won't work either, as mIRC performs a "saveini"-operation on exit. Afaik you'd have to modify the ini with mIRC not running at this moment (/run <some batch file> could work though).