Whirlfloc basically just coagulates proteins...takes smaller chunks and clumps them into larger chunks. You won't particularly get more proteins setting out before you rack to primary or even during the cold break. Gravity still takes time. The whirlfloc is still working on those really fine particulates even when you are still in primary.
Just be patient with it. You might not notice a difference on brew day, but it does make an overall difference through the complete process on the final product.
I personally use nothing but whirlfloc and a 10-14 day cold crash in the keg during carb/conditioning, and end up with very clear beer.
Primary #1 - Midnight Ryeder (Midnight Wheat and Rye)
Primary #2 - Florida Weiss
Primary #3 - Kane-DOH APA (Honey Citra APA)
Secondary #1 - Downtown Flanders Brown (brewed August 2012)
Keg #1 - Raspberry Florida Weiss
Keg #2 - Cinnamon Raisin Cider
Keg #3 - NONE!
Bottled - NONE!