Do you still have the savegame, where the depot is still available?
It would be great if you could send us the savegame to get rid of this crash.
You can upload the savegame to any file hoster like google-drive, skydrive and more.
About the other points, try to generate a new desktop icon through steam, rightclick on Train Fever and there you can create a new desktop shortcut.
About the flickering, do you have an ATI Radeon card?