Why does a long Banner appear below other Banners on later days?

Why the position changes

Banners (all-day events) appear in the order of your calendars in the sidebar, so a banner from a calendar higher in the list is shown above the others.

A banner that spans several weeks or months cannot always stay in the same row for its whole span. As other banners start and end on the days it covers, BusyCal fills the space that is free on each day so there are no empty gaps between banners. That is why a long banner can move down and appear below other banners on later days.

This is how the calendar lays out banners, not a problem with the event.

How to change the order

Drag the calendars in the sidebar into the order you want. Banners follow that order wherever the layout allows. See Ordering Events.