Reason - the upper is out of spec. Mostly likely, the barrel extension is too long and the barrel sits too far, when the breech is closed the BGC is too far forwards.
Look at your upper in the picture - the bolt carrier is flush with the upper at the open end. That is not right.
I'd have to disagree.....the buffer should sit just ahead of the 'tower'. If you look at it from the side, you should be able to see the buffer sticking out of the tube a bit. Then when you close the upper on the lower, the carrier, which should be flush at the back of the upper pushes the buffer backwards (preloading it if you will) so that it (buffer) is no longer resting against the pin. If the carrier sticks out past the end of the upper, you wouldn't be able to close it, it would hit the top of the 'tower'.
Added: If the OP's pin conversion kit IS sitting the upper too far forward of the 'tower', it would also have the same effect. However, I can't comment without seeing them (upper and lower) together.
I still think that the buffer reatiner is in the wrong spot (too far to the rear). And you can't measure the distance to the reatiner from the back of the receiver because (if you look at the actual drawings for a lower) the size is taken from the selector hole. What this means is that the back of the lower receiver could be longer or shorter than spec but as long as the retainer hole is drilled to spec with the takedown and selector holes, the buffer will be in the correct position.


















































