Assume we have a character who has a natural fly speed and a class ability that heavily benefits them to jump (with an Acrobatics check)1. Assume they are flying, say 20' above an open field with enemies at various distances both in the air and on the ground.
The confusion comes from the idea that physically we think of jumping as "off of something", while the rules don't actually state this. Additionally, we can imagine a flying creature flapping heavily or some such thing for a jump-like effect through the air.
Could this character make an Acrobatics check to jump whilst they are off the ground flying?
1: The class ability is 3pp that allows use of Vital Strike with extra bonuses at the end of a jump as a full-round action, but otherwise says it functions as an acrobatics check to jump.