Have you tried contacting the signaller (on the open/close doors menu) to see if it triggers a "proceed at restricted speed" message? Also, freight services are at the very bottom of the priority list so it might be the case that you have to sit and wait for another (unseen) train to pass. Check your map to see if there is potential traffic. and finally (but probably more appropriate with scenarios) check the path to your destination to make sure the points are correctly aligned as a red signal can also be a derail warning.
