There has always been a problem with short/light trains on signaled track. IIRC when RDCs first came out I think B&M had a bad wreck where a few RDCs stopped on sand and then got rear ended by a conventional train on a false clear.

The fewer the wheels and lighter the equipment, the more chance it may not consistently shunt the circuit. Some railroads have specific dispatcher rules for handling things like Sperry cars or trains/engines with a limited number of axles in signaled territory, the dispatcher reuired to further protect them.

Then again, there are plenty of LRT systems that seem to get their signals to work. Caltrain would not be comparable, whereas the Sprinter might be a better example. And remember they are trying to integrate a signal system, PTC and overlapping grade crossing approach circuits at the same time. It doesn't take much to screw things up. I wonder what penalty the contractors are facing, or if it is a design or component issue? That's the problem with today's version of transit railroading -it is far too complicated and the technology being demanded now isn't simple and proven.