If you are using a CO2 manifold with shut-off valves, those valves may have "check valves" inside that would prevent a keg holding pressure to vent back through the CO2 connection to another keg. Hence, you could have one keg empty but the other two could still be pressurized.
That said, there are other reasons why one tap would have "zero beer" while the other two are still dispensing: the "zero" keg could be empty, or frozen, or its beer line could be frozen, or clogged with something like hops.
Try swapping the "zero" keg beer line and gas line to one of the other two kegs and see what happens...
Cheers!