Are you using a switch anywhere with multiple computers hooked up to it? A switch splits connections according to how many PCs you have, for example a gigabit switch with one computer will offer (theoretically 1gb, 99.9999% of the time you will never hit that) when a second RJ-45 is used it splits off to 500mbs each, and a third to 333mbs per computer.
If you do not have a physical separate switch outside your router the multiple RJ-45s on your router operates the same a switch. There are WAY to many factors as to why you will not get 1gb speeds.