Hi Marko,
1.- You write "The funny thing is when you have the Single-answer Multiple choice GIFT format question such as:-----------
Banana is {
=yellow
~%-50%white
~%-50%black
~%-50%blue
} The total score, if the student ticks all the answers, is negative 0.5 (or -0.5)."
In a single-answer Multiple Choice question it's impossible to tick all the answers, single-answer produces radio buttons, and only ONE choice can be selected.
2.- Your problem has nothing to do with the GIFT format. If you create your question directly using the Question editing interface provided by the Moodle question bank, you get the same result.
3.- This is debatable (and has been debated in this forum) but from a pedagogical point of view I maintain that it does not make sense to award negative points in questions and quizzes.
Joseph, once a teacher, always a teacher 😉