It was very confusing when troubleshooting, but probably not important to fix (or it's an XNet issue). When using The Collision Chamber CustomMachine with Molten Lead and Proton Fluid, the products are Proton Fluid, Anti-proton Fluid, and Molten Lead (in order). While Pipez extracts with filters correctly, XNet will not extract Anti-Proton Fluid or Molten Lead if there is and Proton Fluid in the output. It will also not extract Molten Lead if there is either Proton Fluid or Anti-Proton Fluid.
It was very confusing when troubleshooting, but probably not important to fix (or it's an XNet issue). When using The Collision Chamber CustomMachine with Molten Lead and Proton Fluid, the products are Proton Fluid, Anti-proton Fluid, and Molten Lead (in order). While Pipez extracts with filters correctly, XNet will not extract Anti-Proton Fluid or Molten Lead if there is and Proton Fluid in the output. It will also not extract Molten Lead if there is either Proton Fluid or Anti-Proton Fluid.