I have received your sanitized return, and I see what TurboTax did (although I am not sure why in some cases).
On the 1040X:
1, column A - this is the gross wage that your employer would have given you, had you not had an HSA employer contribution (code W in box 12 on your W-2).
1, column B - the code W amount
1, column C - the actual AGI on your 1040, Line 11
*** so actually, your 1040X is starting off correctly, subtracting the HSA amount was confusing but the result in 1, column C matches your 1040, line 11, so it is correct.
2, columns A and C - these are the correct standard deduction, with no changes made.
Lines 3, 4 and 5 follow what happened in line 1 - odd looking, but correct.
I haven't been able to reproduce the tax on line 6, column A (its using the Qualifying Dividend/Capital Gain worksheet (but I can get to that number in line 6, column A, but not exact. But in a sense, it does not matter, because the number in line 6, column C is exactly the correct tax from line 16 on your 1040.
As for line 10 on the 1040X, I have been unable to locate the amount in line 10, column A - the only thing is that it is about 10% of line 4 on the Qualifying Dividend/Capital Gain worksheet (i.e., the Qualifying Dividends and Capital Gains backed out of your income so that they can be taxed separately). Again, it's no matter because line 10, column C is the same value as line 23 on your 1040.
The net result is that column C on your 1040X is matching your current return before you make any changes, so that is correct. That being so, don't worry about the changes made in columns A and B.
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