You are correct. Only the part of the pension received while resident in NJ would be taxable to NJ. I am unable to duplicate your experience using the information provided.
In my online version in the NJ interview on the page you described, the NJ tax is affected by the amount I enter in the box "Amount received and taxable in NJ". Further, if I check the box "Not taxable in NJ" the NJ tax reduces as well. When I continue further in the "Adjustment" section interview, I arrive at a retirement summary page that reflects the amount I entered in the NJ taxable box earlier.
Try signing out and clearing your browser cache. Here is a link for assistance with that process, if needed.
If the experience continues, repost with the TurboTax product you are using and the 1099R amounts/states showing on your form.
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