Get your taxes done using TurboTax

Yes, TurboTax is the problem. Although rejections come from the IRS and not TT, the glitch lies in how TT transmits the AGI data to the IRS. 
I have said this many times in this forum, but if you keep getting rejections due to the "wrong" AGI even after trying the trick of entering zero, use another software program. I now use FreeTaxUSA. Filing a paper return is not a solution; it's a last resort. Who wants to wait 12 weeks for a refund?