Despite Pentagon's directive, the Texas National Guard still refused to process benefits for couples of the same sex who are legally married, Tuesday.

According to a report by the Baltimore Sun, the Department of Defense has officially announced that it will start granting benefits to couples of the same sex who are legally married by September 3.

"It is now the Department's policy to treat all married military personnel equally. The Department will work to make the same benefits available to all military spouses, regardless of whether they are in same-sex or opposite-sex marriages," Defense Secretary Chuck Hagel wrote in a memorandum distributed with the press release, reports the Baltimore Sun.

However, Alicia Butler from Austin, Texas says she was rejected when she applied Tuesday at Camp Mabry. Butler, who is legally married in California to National Guard, Judith Chedville, was told to apply at another facility run by the federal government instead.

"We were told that Texas would not register us into the system and would not issue an ID card for me. We were told that if she was in active duty they would do that for me, but not for a National Guard member because she's part of the Texas National Guard," Butler told the Washington Blade.

According to a leaked guidance by the American Military Partner Association, an LGBT group, the refusal to process benefits was mainly due to the Texas's state's constitution which prohibits gay marriage.

"The Texas Military Forces (TXMF) is a state agency under the authority and direction of the Texas state government," the guidance states. "Therefore, the TXMF must consider that the Texas Constitution and Texas Family Code 6.204 conflicts with the Department of Defense (DoD) policy extending benefits to same-sex spouses. Due to this potential conflict, we are unable to enroll same-sex families into Defense Enrolment Eligibility Reporting Systems (DEERs) at our state supported facilities until we receive legal clarification."

Instead, legally married same sex couples are advised to enroll for the benefits at federal government-run facilities. In the case of Butler, she was referred to Fort Hood, a one and a half hour drive from where she lives.

A spokesperson for Pentagon, Lt. Cmdr. Nathan Christensen says that all states should adhere to the policy, including Texas.

"All Federal Military installations in Texas will issue IDs to all who provide a valid marriage certificate from a jurisdiction that recognizes same-sex marriage," Christensen told the Washington Blade.

ABC News also reports of the same situation in Mississippi where only National Guard offices on federal property are accepting applications. Mississippi, like Texas, constitutionally bans same sex marriage.