On the adapter it says Jumper JP1 Start Buttons as F1 fire 1-2 & 3-4 enabled, 1-3 & 2-4 disabled. I did not want my start buttons as my fire buttons since I have fire buttons, so I placed the jumped across 1-3, and 2-4. However, this doesn't just bypass using start buttons as the two fire buttons, but based on continuity tests and visual inspection of the traces, it actually links fire 1/2 together and start 1/2 together due a huge design flaw from the engineer at jammaboards.com (or whomever they contracted). Unbelievable.
Simply not using the jumpers fixed the fire buttons, but I've gotta take a closer look at the start 1, start 2 traces. Now start 1 still does start 1 & 2 and start 2 does nothing.