Hi chensa,
I think I understand what's going on and will try to explain it here.
Normally, Crescendo will append the new bar to the same line if the line still have space left. However you can't see the space since the last bar must be stretched to fit the whole line. For some reason, or maybe a bug can change the space size without noticed. Therefore the new bar can no longer be fitted in the line and must be put into a new line. However the same thing happens so the next new bar creates a new line again.
One thing I've notice was that this could happen if you selecting one of the note tools. Try cancel the tool (by right click or press ESC) before you appending new bars.
Also, something you can do if this happened - in fact, you can still change the actual size of the bar manually even if the bar is stretched to fit the whole line. You can changed the bar size of the last bar by dragging the bar line, as any other bars. When you holding the mouse button, a dashed line will indicates the actual size of the bar. Just that when you release the mouse button the dashed line become invisible. In this case, you'll have to shrink the bars on both upper and lower lines until they small enough to fit in a single line.
Hope this helps.
Regards