Was part of the fix adding a "Deactivated: Error (invalid train)" message? With the Multiple Unit Train Control mod, I can make it spam that message.
If the player is riding a locomotive with the FARL module installed, and couples to another locomotive forming an MU pair, MU Control will replace both locomotives and kick the player out in the process (it preserves the equipment grids, so the FARL module is placed in the newly placed locomotive). The replacement kicks the player out of the locomotive, but the FARL GUI stays visible even though I'm no longer in a train, and the "Deactivated" message appears once per second until I mine the train that I was kicked out of.