This is driving me crazy. I can't ship from New York to Trenton. Trenton is blacked out, even though I have a direct rail link between New York and Trenton.

I'm not the only one who has had this problem:
"When choosing a route for a particular train, players are taken to a map that shows the available towns with depots. These towns are displayed as small circles. Players choose the towns in the order they want their trains to make stops in them. The problem arises when certain towns can’t be chosen for the route. For instance, many times I had a straight line of track between three or four towns, A-B-C-D. For some reason, I could choose a route from A-C, but not from B-C. Sometimes it would let me choose A-C or –D, then back again to B. The manual only stated that a possible reason for this could be a lack of a clear route for the train. This wasn’t the case, as this particular track was a straight, continuous line with no interruptions, sharp turns or Y breaks. There would be no visible difference between this section of track, and another identical one that would allow this type of travel. I don’t know if this problem was due to some type of bug, or if there was something about the signals at the depots failing to connect correctly with the track as laid down. The manual doesn’t say. The only solution is to delete the trains and tracks, and try again. Sometimes this works, sometimes it doesn’t. The forums have a few people reporting the same problems, but so far no one has suggested anything that works besides deleting track and rebuilding."

I'm not the only one who has had this problem:
"When choosing a route for a particular train, players are taken to a map that shows the available towns with depots. These towns are displayed as small circles. Players choose the towns in the order they want their trains to make stops in them. The problem arises when certain towns can’t be chosen for the route. For instance, many times I had a straight line of track between three or four towns, A-B-C-D. For some reason, I could choose a route from A-C, but not from B-C. Sometimes it would let me choose A-C or –D, then back again to B. The manual only stated that a possible reason for this could be a lack of a clear route for the train. This wasn’t the case, as this particular track was a straight, continuous line with no interruptions, sharp turns or Y breaks. There would be no visible difference between this section of track, and another identical one that would allow this type of travel. I don’t know if this problem was due to some type of bug, or if there was something about the signals at the depots failing to connect correctly with the track as laid down. The manual doesn’t say. The only solution is to delete the trains and tracks, and try again. Sometimes this works, sometimes it doesn’t. The forums have a few people reporting the same problems, but so far no one has suggested anything that works besides deleting track and rebuilding."