No, this is just the limitation of handicap racing. 

It would have been in the. Nor and the boat chose to enter. So fault? 

I suppose it would be possible for a sufficiently biased RC to engineer class splits as to favour individual boats or classes, even more so if course selection and handicaps were brought into the mix. I do recall an incident where an RO said, when queried about a bizarrely penal handicap my class had been given for an event, stating that he had heard we had won everything at a major event a few miles away, and didn't want it happening at his club. What made this particularly amusing was that the style of course set for the first event particularly favoured our boats, and the style of course for this gentleman's event completely precluded such a happening.

I suppose if the bias were malicious and sufficiently egregious and blatant, it might just shade into misconduct under RRS69, although it seems a stretch. Maybe if there were significant cash prizes. But otherwise I agree with Michael, this is the nature of the game. Every -or at least most- dog has its day. Its not an improper action to set class splits or even courses that favour some boats over others for handicap events, indeed its pretty much impossible to avoid. 

Rrs 69 is against a competitoror suoport person, not a raceofficial. 

I'm not familiar with PHRF but I think IRC is a similar system, classifying a broad range of cruising and racing ballasted monohull keel boats for competition by providing ratings comprising single figure allowances based on time.  It provides the following guidance to race management.  "With the ever-increasing range of boat types racing under IRC, it is inevitable that courses and conditions will affect race results. Race Committees can minimise these effects by considering carefully the types of courses set. Conditions are beyond the control of a race committee, but even then course location may be significant. ... Noting also that a balance of course types is a fundamental part of fair yacht racing, it is strongly recommended that race committees should set a variety of courses. For IRC regional or national championships this should be stipulated as a requirement."  There  is more detailed comment in Section 5 of IRC Race Management 
As both a competitor under IRC and race official, I have no issue with conditions in some races favouring one type of boat over another, but in a series running over the course of a year, expect that every boat will have its day, provided the race official follows the guidance of setting a variety of courses. 
What can be an issue is the safety argument: on a day with marginal conditions, heavy boats could compete safely and do well but the race organisers abandon races because it is perceived to be unsafe for light boats (though some do cope well), and in light conditions, the light boats are favoured.  

You'll need to race under ORC in order to use a boat's polars plus have the Rc use the right scoring option in order to more fairly level the playing field. If you sign up to race under a flawed/simplistic , one-number handicap system you accept its inherent limitations.