I have a 1099R with an amount box 6. The amount in box 6 does not seem to affect the tax due. Can you explain?

[MichaelL1]

Box 6 see below from IRS web site.  Hope this helps, but based on what I am reading you have some securities held inside the IRA that have gone up in value and are not sold. 

Box 6. If you received a lump-sum distribution from a qualified plan that includes securities of the employer’s company, the net unrealized appreciation (NUA) (any increase in value of such securities while in the trust) is taxed only when you sell the securities unless you choose to include it in your gross income this year.

 If you did not receive a lump-sum distribution, the amount shown is the NUA attributable to employee contributions, which is not taxed until you sell the securities.