Combine the squash, 1/2 cup water and a pinch of salt in a large microwave-safe bowl; cover with plastic wrap and pierce to vent. Microwave, stirring once, until just tender, 15 minutes; drain.
Meanwhile, melt 2 tablespoons butter in a large nonstick skillet over medium heat. Add the onion and a pinch of salt and cook, stirring, until soft, 5 minutes; stir in the chili powder. Add the beans, rice and 1/2 cup water and simmer, stirring, until the liquid evaporates, about10 minutes. Transfer to a bowl and cover to keep warm.
Wipe out the skillet. Lightly beat the eggs in a bowl with a pinch of salt. Melt the remaining 1 tablespoon butter in the skillet over medium heat, then add the eggs and cook, stirring, until they start setting. Fold in the squash and cook until the eggs are set.
Warm the tortillas in a dry skillet or in the microwave. Divide the rice mixture, scrambled eggs, cheese and jalapenos among the tortillas. Fold up the bottoms, then fold in the sides and roll up. Serve with salsa.