Retirement tax questions

I cannot duplicate your issue -- for me TurboTax is not including retirement income in the taxable income on the MS return.

Here is a workaround to try:

1. Go into Forms Mode by clicking on the Forms icon in the top right of the blue bar. 
2. In the Forms in My Return list on the left, under Mississippi click the F107 Worksheet (MS Income/Withholding Worksheet). [The form will appear on the right side of the screen.]
3. On the worksheet, scroll to the Federal Forms 1099-R section.
4. Mark the box that the 109-R is not applicable to the MS return,  [See screenshot below.]
5. To return to the interview, click on the Step-By-Step icon in the top right of the blue bar.  

@scottg29