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Are these bonds included in 760 Line 1 Federal AGI - did you do anything else with the input related to savings bonds such as exemption for educational use etc?

 

Couple other things I would try before going down the "report a bug" path to confirm it's not some data issue in your return - input a test 1099 (and delete it later) with only simple Box 3 income and see if you get the same effect consistently; and delete the 1099 with the EE bonds and re-input it.