My client received 1099-R for IRA distribution of silver bullion.

nothing was sold, she withdrew it .   I have reviewed the form 5329 to see if there are any special bullion rules as to this and looked at many IRS articles (maybe not the right one] She put her own investment into IRA, the basis of her silver has gone up. They are saying that the full amount is taxable. 
client states that this is not realized, was not a sale, and was told she should have no tax as it is not a retirement withdrawal ???  Not sure what to make of this and where to research, other than asking client where she got the information. 

any suggestions.    Thanks in advance as always.

judy