Ok.
For anyone else having the same problem, you have to change two things in the database for the shuffle to work. First in mdl_question 'questiontext' change MULTICHOICE to MULTICHOICE_S (MC to MCS) and also in mdl_qtype_multichoice_options change 'shuffleanswers' to 1 for questions with the same questionid number. Admin replace tool works for the first part but you still have to turn the shuffle on in the database.