Try thinking about a diminshed chord as 1-b3-b5-bb7 (bb7 is in reality the 6) in it's construction and your software is most likley making a distinction between what is really a -b5 ("-" means minor) chord with no b7 or in most jazz charts it would be a half diminished chord which is marked as o with a slash through the circle (and almost always has a b7) versus a true 4 tone diminished chord with the bb7 (Co). I find in my playing and notation that while I do occasionally play three tone "diminshed" chords I find it usefull to be able to distinguish what the chords are in a pratical sense. Their are many schools of thought on notation and I am sure all are useful and so is your software because it gives you a clear choice on note selection. Diminished four tone chords and half dimished chords are a wonderful thing and the Inversions sound great when building tension in a song and/or moving into another position.
Have Fun, Sky-Coyote the Jazzin' Hobo