I Got A Surprise Phone Call Today

I got a surprise phone call today from the hiring coordinator for the company I recently did Customer Service training for. The IRS is hiring for positions beginning January 2012. The training starts September of this year. I went through a phone interview and I have been given a conditional letter of hire, pending a background check. I am wondering if those Federal agencies like the IRS would refuse to hire you if they find out what your former status is during the background check? The agency I trained with know my status, but I am just nervous over how intrusive they will be as the actual employer. They say it will take 45 days for the vetting process. I am hoping they won't give me a hard time over it like some State governments would. I have worked hard to become who I am and I hope these people respect that.