Oops. Also need to remove the '#' comment character in front of generate_cover_settings.
If you want it to effect all sites, put it in the [defaults] section. Otherwise, put it in the section for the site you want to effect:
Code:
[www.fanfiction.net]
generate_cover_settings:
${category} => Buffy:? [tT]he Vampire Slayer => BuffyCover
${category} => Star Trek => StarTrekCover