Whenever I put a wooden pipe on the right side of a furnace, it either takes out nothing at all, or takes out the fuel at the bottom. Wooden pipes work on all other blocks, like chests and quarries. I will post a screenshot in a minute...

Hi, sides have changed. at the bottom it takes the result, in the sides the fuel

Wow. I'm either a total noob, or never heard about that. (Probably both >D)

The change was made to make pipes behave the same as the vanilla hoppers