Brake pedal soft and hissing noise

My rear brakes were worn out(correction it's just over 100,000 miles!) And took it to a shop and they replaced the rear calipers, rotors, and pads. Driving it home it felt different but I didn't notice it until the next day. When pressing on the brakes they were not engaging until the pedal was extremely low, almost but not quite to the floor. I took it back to the shop and they bled the brakes (they claimed twice) and stated that they could not find any leaks anywhere, but they heard a hissing noise coming from the front and suspected a faulty master cylinder. I had to take the car as it's my only form of transportation, and since then have found that when the engine is off, the pedal has resistance to it, but when the engine is on it loses the resistance yet can sort of be "pumped up" to build braking pressure but not very well. The hissing noise is continuing leading me to believe it might be the brake booster. I've heard other Scion TC owners say they had the same issue and even after replacing the master cylinder and other parts, so I feel as if maybe it's something more simple like a seal or air in the system somewhere. I'm taking it back in this week, but don't want to be raked over the coals if it's something as simple as air in the system or a caliper hanger. Please Help!