Not too sure of your circuit but I would try and have the sound modules trigger an RS flip flop and then time the interval between these flip flops being set. This removes any problem with the trigger signal rapidly turning on and off due to successive peaks of sound.
However if you think about the rise time of the sound waveform, this is going to be in the same order of magnitude as different time of arrival. It is this that makes it difficult.
Yes it will also depend on the gain / sensitivity of each audio channel.