Although the site you are using probably uses MathJax, this issue you are having is unlikely to be a problem cause by MathJax (this is a MathJax forum). It is most likely something to do with the testing software itself, not the mathematical display that MathJax produces. You will need to contact the University to investigate that. Your instructor is the first step, but if he or she is accusing you of cheating, then that may not work so well. You may need to move up the chain to the department chairperson, or to a Dean (do you have a Dean of Students, or a Dean of Studies, or some such thing?).
Good luck with your situation.