On service N542-A with a GP38-2 taking a coal train to load up with coal, there is a bug with the signal passed at danger. You spawn in with the train in front of a switch, halfway through a signal. The signal ahead of you is two miles ahead and at danger (red). When the end of your train passes the signal your train is halfway through (which is red because YOU ARE ALREADY IN THE BLOCK), the game considers you to have passed it at danger and results in a failure of the service. It shouldn't be considered a SPAD for the end of your train to pass a signal your train is already through, and it's unavoidable because it's the first service for that train and it spawns in halfway past that signal.
Sounds similar to the issue I have the AC4400CW scenario, N542-A, you begin the scenario (I have tried requesting signal pass at danger to try and alleviate the issue). It is physically impossible currently, to complete the scenario sequence from the beginning as you run into issues with the SPAD as you near the end of the train.