What should I do if I've been married for 2 years, have yet to receive BAH, and feel like I'm being neglected because I'm gay?

No one is gonna give a shit that you're gay. And, unless you have direct proof you're being neglected/ignored because you're gay, please do not throw that accusation around lightly. But on to the topic of your BAH, have you spoken with your 1SG and Commander? Have you spoken with your BN CSM thru the Open Door Policy? Besides resubmitting the paperwork multiple times, did you at any time speak with your Leadership (from Team Leader to Commander) and get them involved?

If you have hard evidence (video, written, recorded) that you have been discriminated as a result of sexual orientation, then absolutely make an EO complaint and drive that train. We do not tolerate that in our DOD. This complaint will be investigated to its fullest and people will get you answers. The other side of the coin that if it is not substantiated and senior leaders were accused, that might not go so well. I will add some advice here, everybody in this world has prejudice and are judgmental, none of us are perfect. Share with people what you want to be judged on and in this army as an infantry soldier, that is the ability to shoot, communicate, and move on out. No where in working to get your EIB does it ask very personal questions. Sure people will find things out and you should not try to keep secrets but the other side is only my close friends and family know my religion and politics, if you come into my office nothing is here that will clue you in on the gender of my spouse. I will admit this comes easy for me as for years I have been a bedside RN and firmly believe in the strictest and most professional nurse-patient relationship. Most important things to be in how I am judged in this life is as being a Registered Nurse and a field grade officer in the US Army.

Get the fuck out of here with that shit. No one is neglecting you because of who you slept with. There is some glitch. It happens. Figure it the fuck out and stop trying to be a victim. If you show up in the foxhole, no one gives a fuck who you love.