Are you sure the nondividend distributions are included in the box 1 figure on your 1099-DIV?
I use Ameritrade, and for my WPC dividends, the nondividend distributions are not included in box 1a. Ameritrade provides the detailed breakdown of each dividend (e.g. qualified dividend, unrecaptured section 1250 gain, nondividend distribution, etc.) further down in the 1099 document. And I have not recouped my original investment in WPC via the cumulative nondividend distributions.
I highly doubt that different brokers would fill out the 1099-DIV boxes differently. And unless you've held the securities for a long time, it's unlikely you've recouped your investment.
Thus, I'm confident you should not manually subtract line 3 from line 1a before entering line 1a into TT.
