Assuming that you are in the American platforms, you have two separate towed arrays. They have differing capabilities. One works better at slower speeds and shallower depth while the other works better deeper and faster. Along with all of the other variables that Banryu mentioned, this can also be a factor. Likewise, the distance your towed array is away from the boat can make a bit of difference.
Another question that needs to be asked is if you have any mods installed as most of the mods alter the sound profiles of all of the platforms drastically.
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