Improper vertical note alignment and ledger lines too short

1. In the attached images from programs MuseScore 0.9.4 and Igor Engraver 1.7 respectively, one can see that MuseScore in the whole-note chord sets C5 and G5 straight under C6; the correct setting is aligning them to D6 like in the half-note chords of the same example.
2. The ledger lines in the MuseScore example are too short; they should be like in the Igor Engraver example.