I think I found a bug in 9.9. When I change a timetable via the Line-Management "Mirror Schedule" is activated without clicking on the box. When I try to deactivate it the change isn't saved. Using the Schedule-Window of one of the convoy of the Line to deactivate "Mirror Schedule" and creating a new line afterwards doesn't work either. Instead the game crashes :-(.
I think you should warn everyone not to overwrite their old save games until this is fixed.
Thank you for reporting this. This seems to be related to this (http://forum.simutrans.com/index.php?topic=7487) bug, which is now fixed.
9.10, incorporating a fix for this bug, has now been released.