Thanks for the reply.
Added a dummy Not gate, the exact same problem occurs.
I then removed the dummy Not gate, uncommented the 3 other gates from my code, and changed "out=out" to "out=c0" in the first And gate (ie. changed the code back to the entire implementation). Ran the test script, adding output for c0, c1, c2, and c3. This is the result:
Something really wonky appears to be going on, none of the first 3 gates in the code seem to be working at all? The Xor gate is acting differently than from before as well...