On the federal level, sexual orientation can impact how much someone pays in taxes.

That’s because due to the Defense of Marriage Act the IRS does not recognize same-sex couples (marriage, civil unions, registered domestic partnerships) for tax purposes – benefits and deductions afforded married heterosexual couples are not available to gay couples.

Last year the IRS attempted to remedy just one of these disparities for gay couples living in states with community property laws (California, Nevada, and Washington) with a very complex new tax filing system.

It was an attempt at fairness. But as we predicted would happen back in January, the change created a litany of expensive headaches for gay couples.

The latest problems caused by the change have led the IRS to do something you don’t hear very often: issued an apology. That’s the subject of my column. 

To report this story I spent days in lengthy conversations with more than a dozen couples and tax experts. Only a few of those interviews wound up in the story, but they needed to be done so I could authoritatively go the IRS. That’s what led to the apology.

While doing all that reporting I learned that there’s a passionate fight happening largely outside of the spotlight over gays and taxes, and it has national implications for the entire gay rights movement.

Many of the leaders of this battle are right here in the Bay Area.

At the forefront is Patricia Cain, a law school professor at Santa Clara University and leading expert on same-sex tax law. She’s been studying (and advocating) on this issue since 1991 - her blog  is required reading on the subject. In fact, Professor Cain is so far out front on this issue that while I’m writing about one problem she’s already working on the next snag gay couples will face (self employment tax snafus, FYI).

“Federal tax laws have failed to keep up with state property and family laws,” Dr. Cain said. And it’s not just gay couples that are impacted – millions of Americans live in alternative family situations these days not recognized by the IRS.

If Dr. Cain is the general in this fight, she has a battalion of accountants, lawyers and tax experts joining her in battle.

Among them is Mary Anne Courtney, an enrolled agent and certified financial planner in San Francisco who everyone refers to simply as “Courtney.” She worked with many of the couples I interviewed, and she’s dismayed the differences between the rhetoric from Washington and reality.

“I just heard the proclamation from the Obama White House saying June is LGBT month. That’s great. That’s my president. Now tell the IRS,” she said.

Lawyer Deb Kinney is also a distinct voice in this fight. Between personal appearances and online seminars, she estimated that she and her peers reached about 6,000 gay taxpayers and their accountants to instruct them about the recent IRS change. “We did as much as we could,” she said.

Why such a huge effort?

There’s more than just the current tax mess at stake.

Americans have a heightened sense of fair play. Not everyone agrees that same-sex marriage should be legal, but most people think that everyone should be treated equally when it comes to the IRS and taxes. Gay rights advocates believe that a majority of Americans will conclude it’s fundamentally unfair that gay people are taxed differently than straight people.

Opponents of same-sex marriage have seen this argument coming and are prepared.

Tom McClusky, senior vice president of the Family Research Council in Washington, D.C., a faith-based organization that has taken a high profile position against gay marriage, said the issue is not tax fairness, but that homosexuals want rights that others do not have.

“It’s not a matter of equality,” McClusky said. “They’re looking for special treatment.”

The Family Research Council opposes any tax changes that would treat same-sex couples the same as heterosexual married couples. The group argues that the union of one man and one woman benefits society and should be encouraged by the government, and “that homosexual conduct is harmful to the persons who engage in it and to society at large, and can never be affirmed,” according to the FRC website.

McClusky seemed almost gleeful when told about the mess same-sex couples have faced with the recent IRS change.

“They asked for special treatment, so they can’t complain about the complications they’ve received because they got what they wanted,” he said.

So it appears yet another front has opened up in the culture wars, one waged with accountants and spreadsheets.