To amend a second time, and get the proper amounts in Column A,
you must get rid of the 1040X that applies to the first time, meanwhile keeping your revised tax return as the new baseline for the second amendment.
Amend again using the revised return as the starting point. The Form 1040X should then reflect your second set of changes.
If you are using the CD/Download version, saving to a new tax return file may be helpful.
Always make paper print copies of the original or revised before starting this.
[Update: Although it all seems reasonable, I found out this doesn't work. TurboTax won't cooperate.]
