There is no "1099-B form" that you file with the IRS. You receive 1099-Bs from your brokers, and the IRS receives copies of all of those.
Information that you enter off the 1099-Bs is transcribed onto Form(s) 8949 with totals off the Form(s) 8949 flowing to Schedule D and a total on Schedule D then flows to the face of Form 1040X. These are the forms that are provided to the IRS, along with any other Forms or Schedules that may have changed from your original "as filed" income tax return.
It's not clear exactly what your computer problem is. Are you trying to download the "amend" PROGRAM onto your computer and can't do so? You might try calling TurboTax support to see if they can lend a hand as certainly the easiest and safest way to do an amendment is with the program. But if you're up to amending "by hand" that certainly would be acceptable to the IRS.
It might also be helpful to understand what the IRS is asking for here. While filing a properly prepared amendment might be one way of answering their questions, it might not be necessary, particularly if there's no material change to your taxable income/tax liability. A well-written letter, suitably supported by documentation might also satisfy them.
Tom Young
