Here is the problem, when you file a 1040X it only shows a summary of the transactions. You must include a corrected 1040 with your 1040X, as well as any other of the forms or schedules that were included with your original 1040, that have changed. So, when they asked you for the completed 1040 and all forms and schedules, you should have sent that to them, with the 1040X stapled on top. The 1040 is your backup documentation for the 1004X.
I hope that my explanation was clear.

