Larry Cavens here
The noise you are hearing is the main burner in operation, now there are two manufactures of these furnaces #1 Hydro Flame which is now made by Atwood the other is Suburban, I have found the Hydro Flame units are more noisy when the burner kicks in and yes it does sound like thunder which is normal/ whereas the suburban units are a little quieter, the reason why is the burner design/ which incorporates a air injection chamber that is fan forced, the air mixes with the propane gas then is burned, the only other thing that would cause noise is a unbalanced blower wheel which would vibrate the whole unit. If this is the case and is still under warranty the unit should be replaced if not under warranty get the blower wheel replaced as soon as possible or you will wear out the bushings in the motor and it will be more costly to repair