I know this thread is very old, but I came across it when trying to solve this problem, and I'm posting my solution in the hope that it helps others in the future.
earlyout wrote:It sounds like your are trying to amend your original return rather than the return that has been amended once already. I had to amend my 2008 return 3X and TurboTax handled it without any problems.
Just make sure you try to amend the return (data file) you amended previously. Don't think of the 1040X as the amended return, it is only a summary of the changes. Your amended return is the data file you created when you amended your original return.
That may be how it worked in 2008, but I ran into the same problem as Smurf when trying to re-amend my 2009 return. In my experience with TurboTax 2009, this is almost
correct, but there is an extra step that has to be taken. To make things clear, I'll use "original" to mean the first return you filed, "intermediate" to mean the first amended return (the one you've already filed), and "final" to mean the new amended return you're trying to generate.
It is indeed important to begin with the most recent version of your TurboTax file (with the intermediate return), but you must then delete the first amendment form 1040X (as well as whatever your state form is, like 540X in CA) without changing anything else--the return should still be in the intermediate stage after this. I did this by "Updating" the Amend section, then getting to the point where it lets you decide not to amend and offers to delete the amendment. This will leave a TurboTax file with the intermediate version of your forms, but without knowing that they were the result of an amendment. You can then start a new amendment, make the necessary changes to your return, and TurboTax will correctly generate 1040X, showing the difference between the intermediate and final versions.
If you do not delete the amendment form, TurboTax will ignore the intermediate version and incorrectly generate a 1040X with differences between the original and final versions.