Yes, there is a TMCC limitation with regard to ditch lights/marker lights failing to illuminate properly on the trailing unit while lashed up. I have an early set of AC6000 diesels with Legacy, and the same issue occurs with the trailing unit's ditch lights while lashed up.
If the marker lights do not illuminate on the F3 while operating as a standalone unit, then it sounds like a manufacturing defect. It could be something simple as a broken or loose wire. If the marker lights use LEDs, it is possible the circuit was wired backwards or one of the diodes burned out.
-John
