When the American Association of University Professors criticizes college administrations for violating the academic freedom of faculty members, administrators sometimes respond that the AAUP is backing politically correct faculty members who don't care about quality. And when those findings are at religious institutions, a frequent refrain from the colleges involved is that the AAUP isn't sufficiently sympathetic to the missions of faith-based colleges.

In reports issued this weekend, the AAUP faulted the way professors were treated at Greenville College and New Mexico Highlands University -- and the nature of the findings may be surprising. At Greenville, a liberal arts college in Illinois that is affiliated with the Free Methodist Church, the AAUP is backing a professor who was fighting what he saw as a willingness of the college and its faculty to move away from religious orthodoxy. At New Mexico Highlands, the association is backing professors whose tenure cases reinforced the views of some on the campus that Hispanic candidates were being favored and that affirmative action goals were denying promotions to deserving white candidates.

At Greenville, the AAUP found that the college violated the rights of Gerald W. Eichhoefer when it dismissed him as a computer science professor in 2004, citing a tight budget and Eichhoefer's performance.

Eichhoefer had been recruited to Greenville in 1998, leaving a tenured position at William Jewell College and taking a substantial pay cut to return to his alma mater. His early reviews were quite positive about his work in computer science. But Eichhoefer -- whose career included work as a supercomputing consultant and a Ph.D. in philosophy at Rice University -- did not confine his campus role to his department.

In an escalating series of communications -- ranging from one-on-one discussions to mass e-mails to the campus and beyond -- Eichhoefer took issue with the college's interpretation of its faith. Generally, he complained that the college was taking a liberal theological position and not enforcing or teaching its faith. His publications not only took issue with general philosophies, but questioned the faith of individual professors and their ability to teach Christian ideas. Several professors considered suing Eichhoefer for libel and administrators found themselves in increasingly public disputes with him.

Based on its investigation, the AAUP found that the college did not follow established procedures for ending the employment of tenured faculty members during times of financial crisis. Those procedures require more evidence of genuine financial distress and also give rights -- not given to Eichhoefer -- pertaining to how dismissals are handled.

While the AAUP was not convinced that the college was truthful about why Eichhoefer's position was eliminated, the association said that it found that "the dismissal was, to some degree, a reaction to his dissentient activities, particularly his perceived lack of 'supportiveness' for the administration." To the extent that these issues came into play, "the administration not only displayed an unacceptably low tolerance for dissent, but it also violated Professor Eichhoefer's academic freedom."

The AAUP report acknowledged that Eichhoefer may not have been an easy colleague to have around and that he may have gone too far at times, but said that did not justify the way he was treated. "Although the content and method of Professor Eichhoefer's efforts to effect a change in the college's religious identity may at times have exceeded norms of responsible academic discourse, and although many in this extremely close-knit academic community were clearly offended by his efforts, most of his activities nevertheless fell within the realm of conduct that should have been protected by academic freedom."

The AAUP said that Greenville had informed the association of "welcome news," including work with faculty members to revise college policies so they are consistent with the AAUP's principles. The college also told the AAUP that it had reached a settlement with Eichhoefer.

Reached at home Sunday, before attending his daughter's graduation at Greenville, Eichhoefer confirmed that a settlement had been reached, but said he was unable to discuss its details. He said that the AAUP had done "a marvelous job" in helping him.

Currently unemployed, Eichhoefer said that he is looking for work teaching philosophy at at evangelical Christian college.

Although the college resolved the dispute with Eichhoefer and agreed to change some policies, it strongly rejects the conclusions of the AAUP report, according to K. Alexander Schmidt, general counsel for Greenville. In an e-mail interview, he said that the college followed its own guidelines for faculty members consistently, and that many of the AAUP complaints come about only because those guidelines aren't identical to those supported by the association. Schmidt also said that the report relied on "unsubstantiated hypothetical reasoning" and that Eichhoefer's rights had never been violated.

The AAUP report "continuously engages in" a form of "'if, then' analysis" that does not prove anything, Schmidt said. The association offered "no evidence" of wrongdoing by the college, he said. "Despite misguided reports to the contrary, academic freedom and tenure at Greenville College have stood on a solid foundation since the college's inception over 110 years ago and will continue to flourish for years to come," he said.

At New Mexico Highlands, the AAUP objected to how Gregg H. Turner was dismissed (shortly after being denied tenure) and the way David J. Wiedenfeld was denied tenure.

Turner was dismissed from the department of computer and mathematical sciences shortly after being informed that he had lost his tenure bid, despite departmental backing. Turner was fired after he went public with his grievances, and after an angry exchange with one Hispanic faculty member who had recently been awarded tenure and who had circulated a mass e-mail praising the university's direction. In his reply, Turner noted that he was among a group of non-Latino faculty members who had been denied tenure and questioned the professor's "moral strategic compass," and said he was glad he wouldn't be around to witness the "next round of summary faculty execution."

In the case of Wiedenfeld, he was denied tenure in the department of natural sciences despite a series of what he characterized as irregularities and despite backing from two faculty panels. Wiedenfeld also said that he was a victim of discrimination.

The AAUP did not offer a conclusive view on whether the professors or others have suffered discrimination at New Mexico Highlands. But the association did find poor relations between the president and the faculty and a widespread perception that ethnicity may trump other factors. In the cases of the two professors, the AAUP found that the dismissal of Turner was not justified and that he was denied due process and academic freedom rights in that he was punished for raising criticism. In the case of Wiedenfeld, the AAUP found a violation of appropriate procedures because the findings of faculty panels at the university were disregarded without clear reasons or an appropriate appeals process.

Whatever the truth of the view that ethnic concerns are playing too large a role in personnel decisions, the AAUP report said, "this perception of ethnic bias, whatever the reality, has cast a pall at Highlands noted by Hispanic and non-Hispanic faculty alike."

New Mexico Highlands officials did not respond to e-mail and voicemail messages seeking comment. However the AAUP noted in its report that it had been sent a statement from the administration indicating that "because the report concerns confidential personnel matters and pending litigation, we are not able to comment on it."