I don't completely understand it yet, but from testing I have a few theories;
1. Navigate to or via - the AI train will try to find a "sprint", given a choice between a track with a 50mph section for three miles and one with a 100 foot 70mph section followed by 20mph for the remainder of the three miles, it will choose the slower track simply because it can go faster initially. Same thing with "up" and "down" tracks, with right handed running it will choose the left track since there are less or no signals facing that direction.
http://www.youtube.com/watch?v=xJb_8UywoRA
I haven't determined exactly why it chooses convoluted paths, but my theory is that it's short sighted and looks for whatever path will allow it to go fastest at the beginning even if it takes longer overall - it will even do silly things like backing up onto the wrong track, running 10 miles the wrong way past the marker, then reversing again to back the wrong way on the correct track to the marker from the wrong direction. :hehe:
Drive to or via trackmark seems to work better overall, near as I can tell it takes the shortest or most direct path when using the Drive command instead of Navigate. Drive is built in but off by default, you have to edit the session rules to activate it. Why, dunno.
PON_Dwarf_Signal_USA_L02_Permissive,<kuid:522774:100020>
PON_Dwarf_Signal_USA_02_Permissive,<kuid:522774:100021>
Those two were made specifically for the problem of AI trains reluctant to enter a yard to pick up a train, place one at each yard entrance with no other signals between the permissive dwarf and the yard track, it will get a red over red signal but proceed anyway since it is permissive.
Sequence I use;
1. Drive to trackmark 1.
2. Wait 5 (or 20 or 30) seconds (needed so it comes to a full stop and don't collide with uncoupled cars)
3. Uncouplez From (car number)
4. Wait 5 (or 20 or 30) seconds
5. Drive to (whatever next destination)
For the pickup, merely drive to trackmark, couple at trackmark works fine as long as there's a car or cars near the trackmark and there are no absolute signals that would make it do something stupid like waiting for the cars it's supposed to couple onto to clear the block so it can get a green to enter the block to couple onto the cars which wouldn't be there if they cleared the block somehow.

Near as I can tell permissive signals are a must, without one at some point it will get a red signal and refuse to go further.