What is the USPTO afraid of?

Current patent laws enable a challenger to request that the Patent Office review an issued patent, for example under an Inter Partes Review (IPR). The law also provides estoppel provisions that apply to the requester so that the requester cannot effectively take two bites at the apple (one at the Patent Office, and another in District Court). At the same time, the Patent Office has developed certain doctrines to focus IPR requests, one of which is the Redundancy Doctrine. Under this doctrine, which considers both vertical and horizontal redundancy, the requester must select only non-redundant grounds for challenging a patent, so as not to waste the Office's resources. 

Complicating matters is the level of review of institution decisions made by the Patent Office, where the decision whether to accept a request for review is discretionary. At the same time, the Patent Office is still governed by the Administrative Procedure Act (APA) which limits agency action in numerous ways, including that an agency (such as the Patent Office) cannot make arbitrary and capricious decisions. 

In Shaw Industries, the Federal Circuit was faced with the interplay of all of these issues. Judge Reyna issued a well-reasoned concurrence that took the Patent Office to task for its myopic approach.  The Patent Office went so far as to deny the existence of the Redundancy Doctrine when there are PTAB decisions discussing, explaining, and applying the Doctrine. Everyone who files IPR petitions knows the Doctrine and strategically prepares their arguments taking it into account. 

Which leads inevitably to the question - why would the Patent Office deny the existence of a doctrine it follows on a daily basis?

As an analogy, consider a situation where an employer is being accused of firing an employee for an improper purpose in at an "at will" jurisdiction. The basic rule of "at will" employment is that an employer can terminate an employee for any legitimate reason, or even no reason at all. Here, perhaps the Patent Office wants to argue that certain requested grounds of unpatentability are being dismissed for basically no reason at all, rather than have to defend against an allegation that the grounds were dismissed for an illegitimate reason.

The lengths to which the Patent Office has gone to avoid judicial review of its actions is extraordinary. To deny the existence of a Doctrine that so plainly exists only validates speculation that the Office has denied petitions for improper (arbitrary and capricious) reasons. The Patent Office cannot earn the public's trust when abusing the very checks and balances that enable its existence.