I found a funny bug in an arrangement I’m working on. I had brass, winds, choral, and string forces grouped, and I could not get the organ to appear in the proper vertical order until I removed all my groups.
It can be a little difficult to drag a player through the list when groups are involved, but if you look closely while dragging, you can see that the blue line that shows where the player will be inserted when you release the mouse button is either drawn offset a little bit to the right, in which case the player will be inserted into that group, or it goes all the way to the left of the panel, in which case the player will be inserted between the groups at the top level.
That I knew, and it would show up correctly in the Players column, but not in the score itself.
The players will show up in the score in the same order they are listed in the Players panel. If that isn’t the case directly after a re-ordering operation (though it most certainly should be) then I would guess that switching to another layout and back again, or closing and reopening your project, would kick it back into the right shape.