Quick update:
I found the culprit and have fixed the issue. In case anyone is interested, the issue is in the function: save_postmeta_box() in seo-ultimate/plugin/class.seo-ultimate.php
In short, the meta_robots_noindex key would be fine. However, the meta_robots_nofollow key would get lost. The code was expecting the key to be “meta_robots_noindex|meta_robots_nofollow” to work properly, but the code was generating only “meta_robots_noindex”. If you add the following if statement above the explode line, it will work:
if ($fields == 'meta_robots_noindex') {
$fields .= '|meta_robots_nofollow';
}
Again, this is only a quick fix and hopefully this will be patched on the next version.
Thanks! I ended up deleting the plugin.