New info - It looks like if it comes out of the TOP of some sort of storage, it works. Out of the side or bottom, it turns into a different block.
Example: I put an ender chest down, and an advanced wooden pipe on top of it. It worked fine. Connected to that is a void pipe to get rid of all the junk. I wanted another pipe coming off of it to go into a pulverizer, and on any side or bottom that I tried to put the advanced pipe on, it turned into a stone block.