The main problems in the thread talking about crystals and serial issues was that the crystal pins need to be shielded from the serial pins. In short, have a ground ring around the crystal/capacitor circuit and have the crystal as close to the chip as possible. Atleast that is my take on it.
My take away from the people having the problems was that the fuse byte change seemed to be the most effective and simple solution. I wasn't seeing the problem on my Boburino 1284P board but changed the fuse setting just as a precaution.