Build Craft version: 7.99.13
Forge version: 1.12.2-14.2.3.1.2582
Singleplayer
Additional information: Everything was checked twice and it still isn't working I even rebuilt my whole system still didn't work, a bug I'm guessing.

Thanks for the report. That is actually the distiller as the refinery is not more. BC oil processing has been completely redone. Here is a basic guide about how the new blocks work: http://imgur.com/a/AXUOX

For your setup in short, you need to extract the fluids out the top and bottom :)

Duplicate of #3737