The problem and how it happens is documented here: https://youtu.be/nQETbaQvo1g

In brief, when the receiver box is being loaded by an anchor cart and the signal from the interlock box changes, the receiver box does not update. However when the receiver box is being loaded by a stationary anchor block it works correctly, and it releases the train as it's supposed to.

A (superflat) world with the setup used in the video can be found here: http://towerofawesome.org/files/railcraftTutorialWorlds/TokenControlledHS-Section.zip
The issue should be easily reproducible.

This might be related to #751.

Update!

Using the commands "/railcraft debug tile receiver" and "/railcraft debug tile controller" outputs the following:

The receiver (the one that gets stuck on red):
Target: [0; -452, 56, 1043] = mods.railcraft.common.blocks.signals.TileBoxReceiver@5b627591, Receiver:Red (mods.railcraft.api.signals.SimpleSignalReceiver@2a29d979)
Rec Tile Aspect = Red
Con at [0; -245, 56, 1051]
Con Aspect for Rec = Green
Con Objects = mods.railcraft.common.blocks.signals.TileBoxInterlock@4e2bd163, Controller:Green (mods.railcraft.api.signals.SimpleSignalController@481cf589)
Pre Rec Aspect = Red
Updating Rec Aspect
Post Rec Aspect = Green
Railcraft Receiver Debug End

The controller (interlock box)
Target: [0; -245, 56, 1051] = mods.railcraft.common.blocks.signals.TileBoxInterlock@4e2bd163, Controller:Red (mods.railcraft.api.signals.SimpleSignalController@481cf589)
Rec at [0; -452, 56, 1043]
Con Aspect for Rec = Red
Rec Objects = mods.railcraft.common.blocks.signals.TileBoxReceiver@288fb0e, Receiver:Red (mods.railcraft.api.signals.SimpleSignalReceiver@c33de43)
Pre Rec Aspect = Red
Updating Rec Aspect
Post Rec Aspect = Red
Railcraft Controller Debug End

Additionally, when using the debug receiver command on the receiver box it apparently forces an update. This causes it to receive the correct aspect and release the train.