Hi Fiona,
In my opinion the scoring system of the multichoice, multiselect question type in Moodle quiz questions is perfectly acceptable. As you have found out, if your question has for example 4 choices, 2 correct and 2 wrong, then correct choices must be given a score of 50% each and wrong choices a score of -50% each... which gives the following scenarios.
Student ticks all four choices: score = 0 (2 x 50% minus 2 x -50%).
Student ticks 2 correct choices: score = 100%
Student ticks 2 wrong choices: score = 0%
Student ticks 1 correct choice plus one wrong choice: score = 0%
Student ticks 2 correct choices plus one wrong choice: score = 50%.
I frankly do not see what else you would consider a "fairer" scoring system.
Joseph
PS.- You might be interested in an excellent explanation of the MULTICHOICE, MULTISELECT scoring logic for the Hot Potatoes software
here.