We had the same problem with our Cane Corso, Bruno (we got him at 6 months) and our OEM (we go her at 3 years through Mastiff Rescue- from a great lady that took wonderful care of Maggie- so I don't belive there was mistreatment).
We went on about our day....loved and joined in when they were playful and let them be when they were timid but took notice of the activity in the house (loud noises, high energy, etc.)and lowered such activity but really acted as if nothing was going on. We are parrot people by nature and dogs were rather new in our lives at the time... this works very well for timid or screaming birds. Turns out it works for our dogs, too. We still have those moments from time to time but it passes in seconds and all is normal again. I think - Just give the puppy time to find out that it is "safe" and I think things will work out well.
Chanda