You should only report the 1099-R for the conversion and then the taxable part will show on line 4b of Form 1040 (if all contributions were after-tax then this would be only earnings). You shouldn't report the gains separately. Where are you seeing the capital gains tax?
To confirm you only made after-tax (nondeductible contributions) to the traditional IRA? You did make any pre-tax (deductible) contributions? What was the basis on your last filed Form 8606?
@chesapo09
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