We had a professional checked our system and confirmed it's not our system's problem.  We called the IRS, and the agent said that they noticed a lot more CPA firms called regarding e-filing rejections in recent weeks.  Unfortunately, there's nothing they can do but asked us to file the paper returns with Form 14039.  I personally feel that it's the problem on the IRS side, but I can't prove it.  I would suggest that you call the IRS as well, so they are aware of the issues.