I kept getting stuck on this error as well, but was finally able to get around it. The issue for me was the that my income in the two states I have to file both rounded up, but when combined the federal total rounded down. Initially I was just trying to submit all the values as they are reported on a rounded basis but this resulted in the system thinking my numbers weren't aligned. For example:
IL income = 500.65 , rounds to 501
NY income = 100.65, rounds to 101
Federal income = 601.30, rounds to 601 which does not equal the sum of the above
The way I fixed this was in the IL state return section, when it asked me how much of my income was from other states, I just changed the correct rounded up number that was auto-populated (e.g. 101 NY amount above) to round down instead (e.g. 100). This made the totals reported in the IL CR schedule sum up to the total federal income on the rounded basis and the error message went away, allowing me to e-file. Not sure why the system isn't smart enough to handle rounding appropriately or understand why the $1 difference might happen, but at least I was able to get it fixed so I didn't have to file by mail. Let me know if this works for you too!
