The question type that you descripe (one option per item, coding 1 to 6) is the "scale" question.
If you choose the multiple choice matrix, respondents can select multiple options per item, and therefore the variable structure has 6 variables per item, and these are 1/2 encoded.
What to do now? Do not change the question type, this will not solve the issue. Instead use your statistics software to recode the answers. Of course, you need a plan what to do is a person chose more than one answer per item.