Not all flows will render a woman niddah. While intellectually we can grasp this concept, for many women it is still difficult to internalize on an emotional level. However, if your rabbi rules that the brown is acceptable, you are not required to, nor should you, consider yourself niddah. By being "strict" with niddah and acceptable stains, you are taking your shalom bayit and your marriage lightly. It is not fair to you nor your husband to unnecessarily consider yourself niddah.
We do recommend abstaining from intercourse until after the flow subsides. This may help ease your conscience, so you do not feel as if you are having intercourse while actively bleeding.
We also recommend that you consult with your physician to try and determine the cause of this flow, and whether there are any measures you can take to prevent it.
Please feel free to get back to us with any further questions.