I had the same issue last year and this year again. The amount on Form 1040 is significantly lower than the amount in 1099-INT. Last year an Intuit employee asked me to reimport the 1099, but it still showed the same amount. She then asked me to send her my files which I did, but never heard back. Turbotax seems to make some adjustment to the tax exempt interest but there is no way of knowing what or why it does that.
