#1. Is train 2 being held up by a another train taking control on a another approach to the JCN?
Which way is the 2nd train coming from left rear/right rear/ front?
I know this one may seem silly but I have done this one so I'll ask to cover the bases. Are you using the RHM or LHM controller and using the correct one for the jcn?
Are the correct signals assigned to the correct spot in the controller?
Which signals are you using? Some sigs are not compatible with Boats systems due to internal script conflicts.
#2. Does this train have any issues with the CH1 JCN on subsequent passes?
#3. Based on this info, your command string may be too short for the left side. Try adding some Drive via commands or something for this side to space them out as any trains on the left maybe "double booking" the controller. Thus shutting it down entirely.
There is a something BOAT put into the system where the use of these ASB commands lets the train see 3 commands ahead in the driver string. If the command for ch1 is inside of 3 commands of its return to the second ch1 command, it confuses everything and shuts it all down. The use of a ASB Block command somewhere in the middle of these two helps, but I found it's best to build the string so the train COMPLETELY clears CH1, runs to another command (I trick it with a "ghost ASB" setup), ASB Block, then put the next instance of CH1. This allows the train to not be seen twice at the same time by the CH1 controller. It would look like this on my driver command bar:
CH1 Left> CH2 rear> ASB Blocker> CH1 rear.... (basic)
This lets the train pass JCN ch1, clear it, move to the ch2 command, pull the rest of the train out of the ch1 clear trigger radius thus removing anything to do with ch1, hit 2, clear it moving onto the blocker command, clear it to CH1 rear command giving a fresh approach @ CH1 again.