What you are hearing is the difference in 'Part Markers'. A Blue marker is subtle and Green is busier. By default, a 3 chorus song plays the middle chorus using the Green markers. The outer choruses use whatever markers you have in your 1st chorus. To change a marker, click on the measure number and it should change from Blue to Green.

For total control over all of your choruses, you can 'Unfold' the song into one big chorus and place the markers exactly where you want them.