I have a theory on this. The 1.Nf3 line seems to have been "derived" from the 1.d4 line. It looks like a transposition with almost the same move orders.

From the fourth move on, they are perfect transpositions (which explains them being tied with the same score). It's still pretty amazing that the Zukertort prevailed like this, and it would be interesting if this transposition ended up transforming into its own unique line, and then outperforming 1.d4! I will probably be running this calculation for the next full week, so will report back on that.
Back to that theory, just like how it shuffles around the second, third, and fourth positions, scrambling their move orders to try and find the highest-scoring sequence, it also shuffles that first move. And in this case, this transposition outscored 1.e4 so it kicked it off the list.
But since I'm only allowing two lines, now 1.e4 will no longer be evaluated. This kind of defeats the purpose of the contest between the two central pawns, but I guess 1.d4 won fairly since this appears to have happened around 33-ply?
By default, Deep Fritz 13 has you evaluating only two lines. But there seems to be a flaw in this if transpositions can permanently displace the other candidate move.
PS. Where it says 9628 kN/s in the screenshot, that is how fast the calculations are taking place. With 8 cores instead of 6, it will spike up to about 10,000 but not higher. This shows that there are signficant diminishing returns with extra cores (so no need to worry too much if you don't have that many cores at your disposal).
Impenetrable thickets.