It really seems that MAC filtering affects both wireless and wired connections. I don't know a workaround to allow all wired connections.
I really never understood the reasoning (on this router) for globally enabling MAC filtering across both wired and wireless connections. For residential implementations, there typically won't be any unauthorized users on the hard line.
Anyway, as MAC filtering doesn't really give any security, I don't know any reasons why it should be used. WPA/WPA2 with a strong password is much better solution.
We live in a densely populated apartment building where there's lots of wireless traffic. The main concern isn't a security breach so much as simply filtering out other wireless devices while allowing visitors to easily enter our network. For this purpose, I found MAC filtering much easier to implement and manage without the overhead of WPA.