Here is why I think it happened, and, more importantly, how other Pastors can learn from my experience.
The old system of Profile references required a minimum of seven written references plus three telephone references. Most Pastors used three of their written references as phone references, but it is still difficult to get seven people to write references for you on a timely basis. The old written references consisted of a checklist (those providing references had to chose twelve positive skills of the Pastor in question) and an option to write a paragraph or two about the person. In twenty years in ministry I never received a bad reference through this system, though I'm sure some of them were more useful in landing me job interviews than others.
The new Profile system provides a series of prompting questions along the lines of those utilized in periodic formal employee reviews. One of the prompts even asks the reference to provide information about aspects of the Pastor in which there is room for growth. I don't think this is a bad format, per se. I once heard a perceptive sermon about how search committees are often looking for a new Pastor who does not possess the weaknesses of the departing Pastor, but they tend to forget that the new Pastor will not be perfect and will have weaknesses themselves. This question could very well help search committees be more realistic about the fact that no matter whom they select, their new leader will be a human with flaws, vulnerabilities and areas where they are actively growing.
I also like this emphasis on growth because I think that the Christian path is one of humbling oneself, soul-searching, and seeking continually to improve, and Pastors needs to model this quite openly and consciously for the people to whom they serve as Servant Leaders.
However, because I have not received one of these forms to fill out, I do not know whether or not they make it clear how the forms are to be used--that they will not be excerpted or summarized, but will be presented as-is to search committees. If you have never served on a Pastoral search team, it can be challenging to understand how to craft a reference that paints a picture of the Pastor that is positive and realistic.
I don't know that it is possible to prevent bad references from happening to good Pastors, but in the future I plan to prepare the people who provide me with references by explaining that theirs will be one of three references presented to search committees that may be comparing me to over one hundred other applicants. I might also provide them with the examples of references from the sample Profiles on the UCC website, and furnish them with my self-appraisal, in which I am asked to answer the same questions about myself.