Steps to reproduce (A):

1. Construct a rail line, with a loader/holding rail combo on one end.
   1.5) The furnace cart seems to work better when the rail ends in a loop
2. Make a train from a furnace cart, and four or five cargo carts (matching the loader)
3. Send it off.
   Not consistently reproducible. Player presence has no effect, this has happened with me sitting in a cart in the train, and without me anywhere near it.

Expected:
They arrive, the furnace cart is moved over the holding rail, and each tank cart is filled sequentially.

Actual:
They can get quite jumbled up, and they're hard to move again afterwards because of the collision logic.

Steps to reproduce (B): (haven't tried this in a long while, observed in 1.2.5, but it's the same basic problem)

1. Construct a high speed rail, consisting of plenty powered HSR.
2. Create a train consisting of furnace cart and a few others.
3. Fire up the furnace cart to get across a set of unpowered rails to arrive at the HSR.

Expected:
All carts maintain their relative ordering.

Actual:
Furnace cart is left behind; it seems limited to a max speed less than the other carts get boosted to by the powered HSR. If the track is long enough, the furnace cart is

Proposed solution/workaround:
Disable the "collision" detection between carts in the same train, relying solely on the link distance to maintain cart spacing (necessarily making that repulse as well, if it's not doing so already.)
This won't fix the underlying bug, but it will make cleaning up after the bug appears a non-issue.

This may affect the planned steam cart as well.

I had also seen this happen when I would a Steve's Carts Advanced Miner and a Chunk Loader in the same train. This was in 1.2.5. This almost has to be collision related. I found that when I let the miner go for a while the chunk loader would often collide with it because the miner would make frequent stops.

I have had little luck with A as such - though I think it's happened like that too. In general, I have bad experiences with furnace carts and trains, and it's worse with any kind of powered track involved.

However,

Steps to reproduce (C):
1 Create the setup in A
2 Let the loop have only one space between the forward and back tracks
3 Let the loader be 2-3 spaces from where the loop turns
4 Send a train of around 5 wagons.

Expected:
All carts fill in an orderly manner

Actual:
While the last wagons fill, the front is oscillating back and forth. If they are at the "far side" of that oscillation when the last wagon is released, I've had them all go back (last wagons reversing, effectively) and had the two segments "merge" back at the switch into the kind of cluster pictured. I have a video of it, have to find out which, compress and upload. The workaround for that was to make the loop an 8x8 square.

It should be noted that collisions between linked carts has always been a fail-fast situation, meaning it drops out of the collision routine the instant it sees that it is colliding with a linked cart. This does however only apply to the immediately linked cart and not the entire train.

Though its possible that the "solidness" feature is the cause since that involves its own collision routine. Try setting B:solid.carts=false in the config and tell me if you still see issues.

I my experiments and observations, this is only caused by either boosting carts or using vanilla switches. Furnace carts probably also cause issues.

Since none of theses are recommended for use with Trains, I am closing this issue.