some cases of married segments will also be ignored or not returned by RT search even if they are legitimately married:
http://www.flyertalk.com/forum/unite...om-search.html
i ran into a case of this lately booking SMF-LAX-DEN-LNK which was all one ticket (married segments) but RT search would not pull it up, instead offering me only more expensive one stop options. had to get at it with multicity/hipmunk.