Arpeggio mark causes weird staff spacing

I've created arpeggio marks that span two staves (piano), and the program works normally, but if I make another change to the score, or save, the staves spread apart. See the attached screen shots and MS3 file.

Also, I've always been bugged by the spacing of noteheads which butt each other at the stems (stems going in opposite directions). It's easy to manually adjust regular notes, but not grace notes — see measure 10.