First-line indentation causes multiple alignment errors.
1) Create a new piano score.
2) Enter a passage for the first two bars (I entered in the first bars of Liszt's Un_Sopsiro.mscz), so that the entire first bar would be stretched out over the entire line.
3) Decrease the layout stretch so that the both the first two bars appear on the first line together.
Multiple alignment issues are apparent, such as the staff-lines not extending to the barline at the end of the first system.
Disabling indentation of the first system fixes these errors.