OK - I did some measuring last night.
I don't have the dimensions in front of me right now, but the bottom line is there is a difference of 1/4 inch from the bottom of the deep frames to the bottom of the deep body. There is also 1/4 inch from the top of the deep body to the top of the frame.
So, when I stack 2 deeps, I get the 1/2 inch space that I have a problem with.
My mediums have the same 1/4 inch clearance on top, but only 1/8 inch clearance at the bottom for a total of 3/8 when stacked - perfect. So I guess I'm going to shave about 1/8 inch from the bottom of my deeps.
I also was looking at some used frames last night and noticed that the mediums were very clean on the tops and bottoms but the deep frames needed to have a lot of comb removed from the tops and bottoms. I'm not sure if this is due to the spacing, or just the fact that they were used in high traffic, brood-rearing areas.