You mentioned that the taxes appeared to calculate correctly originally. When you are ready to file, does the tax liability or refund change or is it that you are looking at a summary and it appears that the wrong numbers are being used to get the tax liability?
If you go to tax tools, then tools, then view tax summary, the breakdown might not be accurate. You would need to look at the D-400 and see that line 13 is actually a percentage of the federal income and not the entire thing. If it is the correct percentage, then it still is calculating accurately.
