This does not contradict what Lewis writes or what I mentioned on my first post. The "proprietary, custom-built trading system." has a lot of infrastructure code to handle the incoming volume, ensure nothing gets dropped, and trades get evaluated. He doesn't seem to have taken the "decision making" part which would have been their secret sauce.
Sure, the modified open-source code might have been protected by GS employment agreement but that doesn't mean that it was their secret sauce. It was infrastructure/boiler plate code.
Additionally the fact that a code has a GS copyright banner doesn't mean that it was all brand-spanking-new GS-unique code. Even Lewis's article talks about the fact that a single file had open-source code and modified open-source code, aka proprietary code. This subtle language difference is exactly how a lawyer confuses the jury and it is difficult to counteract. Remember the SCO Unix v Novell fiasco!?
Lewis brought together experts who reviewed the evidence on record, i.e. the actual source codes submitted at evidence at his first trial and they reviewed it and found it to be derivative open-source code to run queues, and run infrastructure.