I've been fighting this problem for 3 days, but now solved. This is what I did.
Go to Forms (icon in the upper right corner in the blue band). Then choose Form 2210 from the list on the right, and scroll down to Part II. You cannot un-check Line A, and there is nowhere to enter a [WaiverExplanationStatement]. But on Line B there is a gray box on the right that says "Explain". Click on that box and you will get a form for an explanation. Type in "There is no penalty due." Now return to the Step-by-Step (icon in the upper right corner), re-save your file and re-submit your e-filing.
Even though I was not able to put a check on Line B, my federal e-filing was accepted.
From Rakeyser that also worked for me
