student loan default and federal taxes

I would really love some advice if anyone can help me. I took out a loan for school(approximately $3000) which at one point i defaulted on. Four months ago, I entered into a rehabilitation program where I make an automatic payment (double my original payment) each month. I have not missed a payment and have paid over $400 in 3 months. But today I got a letter from the IRS stating that the student loan debt agency was taking my entire joint refund! I cried for an hour. It's been hard for me to come up with an extra $100 a month for this rehabilitation program but I have done so faithfully. Now, I know that since I filed jointly that I can apply to get my spouses portion of the refund back, but my question is this: Can a student loan agency jack my refund even if I have committed to and made all payments for my rehabilitation program? Also, does anyone know how long it takes to get the spouses portion returned?