The change that happened in the quiz is that shuffle used to be a setting that applied to the whole quiz, but in Moodle 2.9, we added the ability to split the quiz up into sections, and now each section is what gets shuffled or not.
It should be the case that when you restore an old backup, the restore process should create one section (since quizzes in Moodle 2.8 were all in one section) and that new section should be created with the shuffle option that was used in the old quiz.
It seems that is not working for some reason, which is a bug. Looking at the code, I can see that most the code required to make this work is present, but a key bit is missing.
Thanks for finding this bug. I created MDL-55454 to track it.