Kara,
Thanks for the explanation. You see, the problem is that usually survey type of activities such as Questionnaire (in Moodle) are supposed to gather data which will ultimately exported to either a spreadsheet or a more sophisticated stats package in order to examine the data and possibly draw conclusions from it. If the questions are shuffled when presented to the student, then this can lead to all kind of problems later on upon export and data-mining.
In your list of survey software you don't mention LimeSurvey. I don't know if it would to what you want, but it's a good alternative to Moodle's questionnaire, except that it would be totally outside of your moodle site, of course.
Joseph