Kesyon
Should I advise the IRS why amounts reported on Form 1099-B don't agree with my Form 8949 for proceeds from short sales of stock not closed by the end of year?
Repons

For most taxpayers, Form 1099-B, Proceeds From Broker and Barter Exchange Transactions should match Form 8949, Sales and Other Dispositions of Capital Assets. You must declare any difference on your return.

Time of Short Sale

If Then
You entered into a short sale on or after January 1, 2011 You'll receive a Form 1099-B for the year in which the short sale closes. It reports both proceeds and basis information related to the short sale at the same time, so amounts reported on Form 1099-B should agree with the amounts you report on your Form 8949.
You entered into a short sale before January 1, 2011 You should have received a Form 1099-B reporting gross proceeds from the short sale for the year you opened the short sale. When the short sale closes in a later year, use the information from the pre-2011 Form 1099-B to determine the amount of gross proceeds from the short sale to report on Form 8949 for the year the short sale closes. For a short sale entered into before January 1, 2011, your broker is permitted, but not required, to send you a Form 1099-B for the year the short sale closes to provide you with information about the short sale.

There may be other times when your broker reports a basis that's inconsistent with your records. The instructions for Form 8949 advise you on how to make this basis adjustment to report your taxes correctly. For more specific rules, refer to Publication 550, Investment Income and Expenses and the Instructions for Form 8949.