The USPTO isn't required to follow court rulings. The MPEP (Manual of Patent Examining Procedure) isn't even updated to reflect what the courts say unless the PTO likes it.
If you don't like what PTO says, you can always just go to your local federal courthouse to sue for your patent. And the PTO gets sued all the time.
The courts are split on the idea of software patenting because the Supreme Court doesn't understand what software is. Nobody alive can reconcile Benson, Flook, Diehr, Bilski, and Alice. There were four Supreme votes in 2010's Bilski that pure software logic was unpatentable but software that changed the hardware to make it work better was patentable and the example of eligibility was linear programming and compression. Only Scalia was smart enough to see the problem there and even he can't articulate why.
The CAFC -- the patent appeals court -- is relentless in overturning Supreme Court precedents against software patents. Known for being contemptuous of the law and harboring a deeply corrupt majority, the CAFC sees software patents as a gravy train for the patent bar and a permanent tax on a major industry for the benefit of the judges and their friends. Their opinions on the most awful abusive patents reflect a pirate's mentality deliberately ignoring cheating to reach the most harmful conclusions.