Though most county probate judges in Alabama are now issuing marriage licenses to same-sex couples, the fight over the matter continues to simmer in state and federal courts, fueled by two conservative groups that have asked the state’s Supreme Court to halt the practice.

The groups’ emergency petition, which was filed on Feb. 11 as some counties began allowing gay couples to marry, has raised a host of new legal questions and prompted lawyers for same-sex couples to file a federal motion demanding that Alabama’s attorney general dismiss the petition.

It has also exacerbated the confusion among the state’s 68 probate judges, who have been receiving conflicting signals from the state and federal judiciaries for weeks.

Many of them are still deciding independently how to proceed: As of Wednesday morning, 48 of Alabama’s 67 counties were issuing licenses to same-sex couples, according to the Human Rights Campaign, a gay rights group.