This has a lot to do with the signaling. The AI drivers will drive at caution speed which is about 1/2 speed when they cannot see a signal, or if there is a junction ahead. I have found that if I place Type 05s along the line before the junction, which has a type 04 and type 06 combination, that the AI will operate at the posted speed. 
My signaling pattern is like this starting with a single to two-track line:
Type 06 facing towards the singla track------ Type 04 on both tracks, facing towards the double track side, then Type 05s facing both ways with one on each track, repeating until I reach the next double-to-single track.
I space my signals about the length of the 3000t US coal train. I use this as my sliding ruler and place the signals roughly at the end of the consist.
Another thing that will cause the AI to operate at the 1/2 speed is a junction facing the wrong direction. If you align the switch properly, then the AI will drive at full speed, but ensure you have the signals in between as well because the AI will default to 29 mph when they approach crossovers and junctions that are protected by type 06s and type 08s.
John