Knowing that you have only a pair of tower speaker is a good start. We need to know what amp.
Does the boat have any other amps, or are the in-boats driven off the head-unit? Are you experiencing any issues with the in-boats? Turning the head-unit up past 3/4 volume runs the risk of clipping the signal going to the amp. This can result in what you may be experiencing. Also, having the amp's cross-over filter set to Full-Pass, rather then High-Pass, can also result in some unpleasant side effects when the volume is turned up. Inputting too mush bass from the head-unit will as well. Poor MP3 downloads can also result in some crappy sounds. The type of amp and/or how its wire can lead to overheating and thermal shutdown. There should be a green light on the amp that goes out and a red light that comes on if the amp is going into protect mode.