i recreated the problem, and here is what i think is happening.
SSS is used for organic materials, and what SSS does, is it lets some of the light pass through an object. i also think that it only uses the surface of a single object, so if one object is intersecting itself, the mesh witch is inside the object wont be affected by SSS. however when they are two separate objects, then the SSS will apare on the whole thing.
and since SSS lets some light pass through, and it now has to go through 2 objects, the amount of light that gets through is minimal. kinda like if it doubles the density…
im not sure, and i might be wrong. the main reason why i actually think this is wrong is because i think you should see a dark shadow around the whole area where the two objects are intersecting, kinda like if they where slightly transparent.
anyway, im not sure. what are you using SSS for? maybe there is an easy way to work around it.