Amended CT 1040X return for CHET contribution

Sorry, for the misunderstanding in your original message you said the 1040X didn't change.

I tried to reproduce this problem and I got a $900 by doing an amendment. Perhaps you didn't do the steps in the proper order. Let start by putting the return back the way it was.

1. Click on Tax Tools near the bottom of the left side menu.
2. Select Tools.
3. Click on Delete a form.
4. Find the CT-1040X on the list, click Delete to the right.
5. Confirm that you want to delete the form.
6. Click Continue and then Continue my Return.
7. Select State from the left side menu, then Continue. 
8. Select Edit to the right of Connecticut, then Continue.
9. Select Edit to the right of Income.
10. Select Edit to the right of CHET Contributions.
11. Clear the box with the dollar amount in it. This will put your return back to the way it was before amending it.
12. Scroll to the bottom of the list and click on Done with Income.
13. Select Edit to the right of Other situations, then Continue.
14. Select Revisit to the right of Connecticut Amended Income Tax Return.
15. Answer the first question Yes.
16. Verify the original refund or balance due, click Continue.
17. Answer No, to the amendment explanation.
18. Scroll down and enter your amendment explanation on the blank lines, click Continue.
19. Click Done with Other Tax Situations.
20. Select Edit to the right of Income.
21. Select Revisit to the right of CHET Contributions.
22. Answer the first question Yes.
23. Enter your contribution in the box. 
24. Scroll to the bottom of the list and click on Done with Income.
25. Select Let's Check it Over. 
26. Continue until the return is reviewed.