If I'm understanding your comment correctly, TurboTax is doing it correctly. The losses are NOT limited to $3000 per year. The losses offset ALL of the gains, PLUS you can use an 'extra' $3000.
Does Line 13 of your Form 1040 show negative 3000? If so, it seems correct to me.
While I do agree that TurboTax has some 'bugs' and errors, you need to be careful about overriding because it is USUALLY correct, and your understanding of things could be wrong.
