For Craig Ross and Richard Cash of Franklin Township, N.J., April 15 was a nightmare beyond what millions of other anxious Americans felt as they rushed to finish their returns. New Jersey allowed them to file their state taxes jointly, recognizing the civil union they entered in 2007. But the Internal Revenue Service refused to allow them (or any other same-sex couple) to file jointly, causing extra paperwork — and expense.

The disparity wreaks havoc on same-sex couples who live in states that recognize their relationships. New Jersey’s civil union law is supposed to give same-sex couples the rights of marriage simply without the name. California, Oregon and Washington State have broad domestic partnership laws akin to New Jersey’s civil union law. Massachusetts, Connecticut, Vermont, Iowa and the District of Columbia actually allow same-sex couples to marry. But the 1996 Defense of Marriage Act, which bans the recognition of same-sex relationships at the federal level, makes tax time uniquely complicated.

“We’re in a Catch 22,” said Ross, a database administrator. “The best our accountant can do is to prepare two individual tax returns for the IRS and then a joint return for New Jersey, and try to figure it all out. It’s three configurations of tax returns compared to just one for a straight married couple.”

The couple’s accountant charged them $600 more than he charged a typical married couple, allowed to file jointly at the state and federal levels. They used tax software in the past, but found it did not take into account the conflict between the state and federal governments’ views of their relationship.

Complaints about the tax disparity are common among same-sex couples who live in states that recognize their relationships, said Sarah Warbelow, a lawyer at the Human Rights Campaign, the nation’s largest gay advocacy organization. And the disparity, she added, goes beyond the extra paperwork.

“Same-sex couples feel very strongly about opposite-sex married couples who don’t have to pay federal taxes on the health insurance for their spouse,” she said. “But if they’re a same sex married couple, they have to pay taxes on the spouse or partner’s benefits as though it were additional income. And that could cost thousands of dollars.”

“Discrimination,” said Warbelow, “hurts your pocket.”

And that includes what married or civil-unioned same-sex couples have to pay accountants. “It is 25 to 50 percent more work to prepare taxes for civil union couples in New Jersey,” said John Traier, a CPA in Wayne, N.J., who has been preparing taxes for clients for 30 years, including for same-sex couples. “The issues are so unique and the software products on the shelf don’t deal with them at all.”

Kathie Sherman of San Jose, Calif., and Olga Ydrogo have been partners for almost 15 years. They got legally married in California in 2008 before voters banned same-sex marriage, and the state still recognizes their marriage.

“We’re spending $6,000 extra a year in life insurance premiums just to cover our taxes should something happen to one of us,” said Sherman. “That should be totally unnecessary because we’re married, right? It’s frustrating.”

Last fall, pro-gay members of Congress introduced a bill in the U.S. House of Representatives, the Respect for Marriage Act, which would repeal the Defense of Marriage Act and provide federal recognition of same-sex couples legally married at the state level –allowing them to file federal taxes jointly. The bill encompasses married same-sex couples, but not those in civil unions or domestic partnerships.

Although the bill now has 109 co-sponsors, Congressman Barney Frank, D-Mass., the longest serving openly gay member of Congress, recently told the gay news magazine The Advocate: “There is zero chance of this bill becoming law in the near future.”

Meanwhile, married same-sex couples in Massachusetts have filed suit in federal district court seeking to invalidate the Defense of Marriage Act as unconstitutional. According to the suit, one of the plaintiff couples has paid $19,066 more in taxes since they got married in 2004 than if the federal government allowed them to file jointly. Another of the plaintiff couples, also married in Massachusetts in 2004, claims to have paid $25,359 more since then.

Aside from the tax disparities, married same-sex couples are also angered by the emotional consequences of not being recognized by the federal government, said Lee Badgett, an economist at the University of Massachusetts and UCLA who wrote “When Gay People Get Married.”

“People value the right to marry so they can make it clear to the larger community that their spouse is a member of their family,” Badgett said. “I did a study of married same-sex couples in the Netherlands, where you do not get very much in the way of financial benefits from being married. And same-sex couples still fought for the right to marry and many decided to get married because they wanted that public recognition.

“Many same-sex couples in the United States have the same motivation,” Badgett said.

They include Marty Finkle and Michael Plake of South Orange, N.J., who entered a civil union in February 2007 on the first day the law took effect.

“I actually can compare apples to apples,” Finkle said. “I was married to a woman and we had all sorts of deductions and other tax breaks. And though Mike and I don’t have them now, that’s not what hurts the most. Every year we are denied the opportunity to file as one, and it is insulting. Any couple would feel insulted.”

Craig Ross agrees. “We’re definitely not entitled to the same rights and benefits and obligations as a married couple would be,” he said. “And each year when we have to file these returns, it’s basically just another reminder of, ‘you’re not married.’”