After seven and a half hours of switching bliss, working my way westward from Havre to Shelby, as I approached Dunkirk, the last station before Shelby, I encountered a passenger train (the EB?) waiting on the main. The switch is set for me to go into the siding. But there's not enough room for me to get past the passenger train, and we collide.

???

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Do you have the signals set to permissive? If so, AI traffic will first stop and then go past the signal, then stop again just short of the track switch (because it is opposed to the AI train), and it will foul the track. If you want to set signals to permissive, then either choose the "No AI Traffic" option when generating an activity, or else follow the suggestion in the AG manual about switching back to normal signals after using permissive to pass a signal.