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The reason why your federal refund is not affected by the backdoor Roth conversion but your state is depends on the state in which you live. Some states make things complicated by abandoning or modifying the federal income tax rules for IRA contributions. Most states impose a state income tax, as is known. However, some states actually do not follow the federal income tax rules for IRA deductions. Instead, no IRA deduction is allowed at the state level.
I am having the same problem. There is a spot on the MA form questioning what the "Other Contributions Previously Taxed by Massachusetts" is.
I went through the steps for the backdoor contribution (https://ttlc.intuit.com/community/entering-importing/help/how-do-i-enter-a-backdoor-roth-ira-convers...) and once I entered the contribution to the traditional IRA, the Federal form removed the taxes as expected. MA did not. The backdoor Roth conversion is more straight forward without having a previous traditional IRA from previous years as there would be a prorated conversion. I had no prior traditional IRA and the federal form is good. I then did the above step after regoing through the MA form questions.
Massachusetts is following the Federal tax rules.
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