There has to be user error in the actions and/or facts presented about the incident. Electricity doesn't have different sets of rules it operates by in any circumstance. If the jumper cables WERE hooked up correctly for the existing battery system, there would be no melted terminal - that is an absolute certainty.
"Something" wasn't correct about the circuits created when the jumper cables were added. For instance, does the boat have a wire connecting the starting NEG to the NEG terminal of the #1 TM battery? (I don't advise this, but some boat owners have such a connection.) If that "Common NEG" cable exists, then the only battery that can be used to jump is the #1 TM battery. Connecting to #2 or #3 will melt something or blow up a battery if there is a "Common NEG". In fact, it will do exactly what you have described as to when the sparks can be expected.