Congress makes legislation. That's only part of law. The judicial branch of government attempts to resolve ambiguities in the legislation. That's what the Supreme Court did in 1972 when they ruled in Gottschalk v. Benson that software for a general-purpose digital computer was not eligible material for patent protection. They were careful to say that Congress should really clarify this question, and that they weren't categorically saying no software could ever be patentable.

Congress has still not clarified this question. What should be followed is Supreme Court precedent, i.e. Benson, Flook, Diehr. Theoretically, that's the law until Congress says something different.

The word of the Supreme Court should be actual law, not just theoretical law. It's up to the executive branch to direct the USPTO to follow that law. Patents should be examined consistent with Supreme Court precedent.

Congress can override a presidential veto with a 2/3 vote of both houses. That cannot be overridden by executive power.

After 10 unsigned days, excluding Sundays, bills become law, unless Congress adjourns before the 10 days expire, at which point it is automatically vetoed—the so-called “pocket veto”: http://en.wikipedia.org/wiki/Pocket_veto

That's true. But, again, though - that requires Congressional action, and Congress is most decidedly not part of the executive branch of the US government. My point is that this is a Congressional (legislative branch) issue, not a Presidential (executive branch) issue.