Does your tax return have a Form 6251 (and therefore an amount on line 1 of Schedule 2)?
Alternative Minimum Tax (AMT) can sometimes be the cause. Effectively, AMT can sometimes cause some of the Itemized deductions to be reversed and added to the AMT tax. If TurboTax sees that, it may choose the Standard Deduction because it knows that AMT will reverse some of the Itemized deductions.
