Are you saying that the ethernet ports between the moca and the router are running at 100mbps or the ports to the router are at gigabit and it is the connection between the moca devices that is not running at gigabit.
If the ports are running at 100mbps it most times is a cable issue.
If it the connection between the 2 moca units that is more complex because there can be lots of stuff between the 2 units. You could try a short coax cable between the units in the same room and see if it will function at full speed in that configuration.