Thanks for all your well-intended comments, but here is what actually happened.
I had two1099's that uploaded perfectly. Two of them had qualified dividends. The total dividend and qualified dividend info uploaded correctly.
I also had cap gains so Turbo Tax calculated my tax using the Qualified Dividends and Capital Gain Tax Worksheet. Turbo Tax did not include both 1099's amounts for qualified dividends in that worksheet: it only picked up one (the smaller one). All the rest of the dividends were treated as ordinary dividends in that sheet, and then on the Form 1040 it did not include all the qualified dividends that were listed on both 1099s. It is a bug in Turbo Tax.
After calling Turbo Tax support, I told them I would simply delete one 1099 and combine all the info from those two into a single 1099 entry. That fixed the problem and I got about $3,450 lower taxes.
I confirmed all the above by looking at the worksheet itself in the details from the return.
