"if I say yes, am I claiming the withheld taxes twice?"
Yes you are. The taxes paid at vesting pertain only to the compensation created by the vesting. Your sale of the stock creates capital gain or loss, an entirely different animal.
Clearly you're doing something wrong, but I'm not sure what. Ordinarily when people post a question like this it's clear to me that they are using the wrong basis to report the sale. (The per share basis of the stocks received is the same as the per share "fair market value" to calculate the compensation, so selling at a small decline in price from the vesting date should produce a loss.) But you say you are reporting a loss?
The only other thing that comes to mind is that you're using the RSA "Guide me step by step" interview and, somehow, inflating the number of shares vested, increasing the compensation created by TurboTax? (Sometimes people do tell TurboTax about the same vesting twice, once when they are reporting the sale of stock "for taxes" and then again when the are reporting the sale of stock "for cash to me." TurboTax looks at that as two separate vestings and doubles up the compensation income.)
IF you do in fact know your basis - same per share number used for the compensation calculation - I'd say delete the trade you're working on and simply reenter it using the "Stocks, Mutual Funds, Bonds, Other" interview and telling TurboTax that no 1099-B was received. You'd then enter information solicited by TurboTax, including the CORRECT basis, and you should end with a loss, reducing the amount of taxes owed or increasing your refund.
Tom Young
