That is an odd problem, because you have a manual focus SLR. It's not unheard of for a lens in a rangefinder system to have a focus offset, and it can happen with some lenses in AF systems due to an interaction with the sensors, but in a manual focus SLR, you're focusing on the actual image made by the lens. If the body's groundglass or mirror were in the wrong place, it would happen with all of the lenses.
Possibilities might include that the lens is shifting a little internally as Matt suggested, or somewhat more exotically, that it has significant focus shift when stopped down to the taking aperture. Focus shift of this kind shouldn't be an issue on a modern SLR lens; if that is the case, then possibly the lens is assembled incorrectly (like incorrect element spacing). Or that there's some other issue and the link to the 55mm lens is a coincidence.