My hunch is that
String[] words = str.split(":");
is probably not returning an array of length 2. Changing the last line of the for statement to
if(words != null && words.length > 1) {
menu.clanowner.put(words[0], words[1]);
}
should eliminate the IndexOutOfBoundsException.
As a debugging practice, it also helps to know exactly what it going in there, so make sure that
List<String> s = getConfig().getStringList("clanowner");
truly is giving you output that should produce arrays of length 2 or more either by debugging or manually inserting values that should work, or both.