In one of the restaurants where I worked, we would cook the filling for 10-15 minutes in the microwave before putting the puff pastry on. We would do an egg wash and top the hot filling and then cook it at 375-400 for about another 10-15 minutes. Cook your filling first until it is almost done, and then top it with the pastry.The cold filling is the reason the center of the pastry does not cook. Because the pastry is pressing against a cold surface it takes longer to get up to temperature. Also your baking temperature may be too low. Most puff pastry recipes call for a temperature in the 400s Fahrenheit.