Just noticed this so sorry to bump.  Have you tried using two instances of junction link for one pair of junctions?  Ie, the first junction link will be junctions 1 and 2 in that order, and the second junction link 2 and 1 in that order?  As long as the crossover is linked I wouldnt have thought further linking the branch junction to the crossover is necessary.
Stupid question as I don't know much about American signalling, but in the second picture of the above post you have a double head signal on what is effectively the short section of bi-directional track. Would it not help prevent conflicts by placing it where the single head signal by the blue loco is?
				
			Stupid question as I don't know much about American signalling, but in the second picture of the above post you have a double head signal on what is effectively the short section of bi-directional track. Would it not help prevent conflicts by placing it where the single head signal by the blue loco is?