Heat a large skillet to medium-heat. Add the pumpkin seeds and cook, stirring and shaking the pan until fragrant and slightly golden, about 4 minutes. (They'll pop a bit as they cook, so watch out for flying seeds!) Slide onto a paper towel on the counter to let cool.
In the same skillet, heat the olive oil over medium-low heat. Add the garlic and sauté until softened, about 2 minutes. Stir in the jalapeños and cook another minute or so. Stir in the chicken broth, turn the heat to medium-low. Simmer until the liquid is slightly reduced and the chilies soften.
Scrape the skillet mixture and pumpkin seeds into a food processor. Process until the mixture is a coarse but spreadable paste. Scoop into a bowl and let cool while you prepare the sauce. Wipe out the food processor with paper towels so it's ready to use for the sauce.
MAKE THE BUTTERNUT SAUCE:
In a large skillet, heat the olive oil over medium heat. Add the leeks and sauté until soft, about 3 minutes. Add the squash and chicken broth, increase the heat to high, and bring to a boil. Reduce the heat and simmer, covered, until the squash is tender (10 to 15 minutes).
Transfer it all a to food processor, adding cumin, salt and cream. Puree until the sauce is completely smooth. Return the sauce to the skillet. If the sauce seems too thick, thin it out a little bit with additional chicken broth.
ASSEMBLE THE CHICKEN AND COOK:
Lay each breast flat between two pieces of waxed paper. Pound until about ¼-inch-thick. Spread ¼ of the pumpkinseed pesto across each breast. Sprinkle ¼ of the cheese over the filling. Fold each breast in half to create a pocket.
Heat the olive oil and butter over medium heat. Place the flour in a shallow bowl and carefully dredge each chicken pocket in the flour. Add to the pan, one by one. Cook until the pink is gone, about 5 minutes on each side. Remove from the pan when cooked.
Reheat the sauce and serve each chicken breast topped with a spoonful of sauce.