Do you not see the screen I posted (or a similar screen)? The selection only applies to the current 1099-R and must be selected for each 1099-R entered. It will always revert to the default (the first taxpayer on the tax return) between 1099-R's. You can edit the 1099-R to verify which spouse that it was assigned to.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
