mind-body relationship
I think the problem stems from a desire to know the mechanistic workings of reality; e.g. how one thing affects or effects another, rather than simple that it does so.  Buddhism is, for the most part, terribly devoid of explanations about the former, since it is ultimately a practical path. As the Buddha said time and again,

Bhikkhus, both formerly and now what I teach is suffering and the cessation of suffering.
-- MN 22 (Bodhi, trans)

In the context of your question, as others have pointed out, there really isn't any problem on the surface: physical reality clearly exists, as does mental reality; they also clearly interact with each other in a manner that is fairly easily definable.
The problem comes when you try to know more beyond these simple facts, i.e. how and why they exist and interact the way they do. These questions are foreign to Buddhism because they are not really useful at all, and moreover are probably ultimately outside of the realm of what can be empirically known.