It technically doesn't (and certainly shouldn't) work. This is the kind of trick that could easily backfire x10 when the DM uses it against you.
Battle Jump desc. states that:
...nor can you effectively battle jump while under the influence of a fly or levitate spell or effect, as you have to hurl yourself down on your foe.
Natural flight is a fly effect, so it doesn't sound like it'd work. You have to not be in the air when the hurling down begins, pretty much.
Dropping from flight wouldn't work for stuff requiring an actual jump, like Leap Attack, since you need to be grounded to jump.
However, there is a way. Depending on your elevation, you can fly up to the mast 5ft above the big guy, make a climb check to get a hold of it, then a jump check to jump down from your climbing position to the square behind big guy to make the charge.