How did you receive the information from IRS saying nothing was paid?

IRS may not show record of it yet....did you send them the copy of the 1099R you received to them to show withholding in Box 4?

I filed a paper return including the 1099r.  I got a response that I owed nothing and had nothing coming back mailed to me.  I should have gotten all of the $$ that were witheld back.  I called the IRS and they told me that nothing had been paid.  I also got a copy of my tax transcript from them and it shows $0 in witholding.

Look at the copy of the 1099R you kept....does it have a dollar amount in box 4?

The 1099-R box 4 withholding should have been added to the 2018 1040 line 16 W-2 & 1099 withholding and also shown on the "Tax Payments Worksheet" line 12 - was it?

If not, then check your 1099-R entries for data input errors.

The 1099-R is correct.  It shows the withholding properly in box 4.  This amount is also carried over correctly to my 1040.  Both the 1099-R and the 1040 were submitted with these figures correctly entered.  However, when I have retrieved my IRS transcript it shows $0 for withholding.  I had a conversation with the firm handling the retirement account for Bose Corp and they pretty rudely told me that they could not provide any help as my 1099-R is proof that the money was paid by them.  However, the IRS says that nothing was deposited on my behalf from their Tax ID number.  The IRS told me to deal with the fund administrator and the administrator told me to deal with the IRS.  I feel hopelessly caught in the middle with no power to effect any change.
Thanks for all your suggestions and any further suggestions will be most appreciated

If the withholding was probably claimed on your tax return then unless the IRS denies your refund (or taxable amount), I would not worry about it.    The withholding may not have gotten properly entered in to the wage and income transcript, but if the bank never submitted the withholding to the IRS then that should cause a processing error on your tax return and generate a IRS letter to you.     

This is a long shot but is the ssn right on the 1099R?