(CNN) -- In the weeks and months following Justice Anthony Kennedy's ringing endorsement of same-sex marriage, couples flooded court houses in every state, buoyed by the ruling.

But in some pockets of the country there has been resistance. A clerk in Kentucky is refusing to grant marriage licenses, other state officials are dragging their feet, and opponents to the Supreme Court's decision are mounting legal challenges, in which, they argue that the ruling interferes with their freedom of religion.

"The great majority of states are readily complying with the Supreme Court's ruling in Obergefell v. Hodges," said Shannon Minter of the National Center for Lesbian Rights.

"But the resistance of some state and local officials is significant," he said, noting that his group and others are having to divert resources. "It is frustrating that we must continue to expend scarce funds to ensure that states are treating same-sex couples and their children equally, now that the Supreme Court has spoken so clearly."

In the hours after the Supreme Court issued Obergefell, one Kentucky clerk, Kim Davis, announced that the Rowan County Clerk's office would no longer issue marriage licenses to any couples. Davis is an Apostolic Christian who says that she has a sincere religious objection to same-sex marriage. Other clerks in the state have expressed concern but Davis is the only one turning away eligible couples.

In early August, U.S District Court Judge David L. Bunning ruled against Davis citing the Obergefell decision.

Bunning said that Davis is "simply being asked to signify that couples meet the legal requirements to marry" and that she remains free to practice her Apostolic Christian beliefs. "However, her religious convictions cannot excuse her from performing the duties that she took an oath to perform as Rowan County Clerk."

Mat Staver, the Founder and Chairman of Liberty Counsel, is representing Davis and recently lost a bid to have Bunning's decision put on hold while he appeals her case. Staver says he is now planning to file an emergency application with the Supreme Court for relief.

"Kim Davis did not sign up as a clerk to issue same-sex marriage licenses," he said. "Her job duty was changed by five lawyers without any constitutional authority. At a minimum, her religious convictions should be accommodated."


In Mississippi, Roberta Kaplan, a veteran litigator who represented Edie Windsor in her successful challenge to the Defense of Marriage Act in 2013 went to Court earlier this month to challenge the state's ban on gay adoptions.

The law reads in part that "adoption by couples of the same gender is prohibited."

In court papers Kaplan writes, "The Mississippi Adoption Ban writes inequality into Mississippi law by requiring that married gay and lesbian couples be treated differently than all other married couples."


In Florida, Cathy Pareto and Karla Arguello, the state's first same-sex married couple, have gone to court for the right to have both of their names listed on their first child's birth certificate. They say that despite Obergefell, the Bureau of Vital Statistics has continued to refuse them the right to have an accurate birth certificate.


Meanwhile in Colorado, Jack Phillips, a baker, declined to make a cake for a same-sex couple for their wedding ceremony because he said it violated his religious beliefs.

The Colorado Court of Appeals ruled against Phillips saying he violated an anti-discrimination law. Lawyers for Phillips plan to appeal the decision.

"Phillips isn't saying he doesn't want to serve gays and lesbians," said Jeremy Tedesco, his lawyer, "in fact he offered to make them anything else they wanted he just said because of my religious beliefs I can't create a cake that celebrates same sex weddings."

In the post- Obergefell world, opponents of gay marriage have increasingly turned to claims of religious accommodation.

"Now that we have Obegefell, " Staver says, "the issue is the extent of the right to have free exercise of religion accommodated."

He points to florists, bakers and photographers in various states that are involved in court battles for religious accommodations.

"These are individuals who have sincerely held religious beliefs and they are seeking the right to be accommodated under the First Amendment. They have the right to have free exercise of religion," he said.

Gay rights advocates are gearing up for the challenge.

"Religious freedom is a core American value we must safeguard," said James Esseks of the ACLU. But he says that religion doesn't give anyone the right to discriminate and when businesses open the doors to the public they must be open to everyone.

"Serving gay people doesn't mean you approve of them, it means you're selling them a cake, or flowers, or a hammer. That's all," Esseks said.

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