Not all songs start with a measure that contains all beats as indicated by the time signature. Some begin with a so called pickup measure or anacrusis.
Typically the final measure is also shortened, so the two partial measures together make a full measure.
Also, when a section of music starting with an anacrusis is repeated, notation standards ensure the rhythm remains consistent during the transition back to the beginning.
Five Lines takes these standards into account when calculating the metronome and cursor timing. All you have to do is to specify the pickup measure length.
The video shows a full example.