I agree with Howard - if you are setting up a new environment, you will be a lot better off to get rid of the bitnami version and start with a fresh version manually installed. This is just going to give you headaches as you move forward and might even be the cause of this issue too.
Back to your problem though. I suspect on the new moodle, you might have either course or user themes enabled and these were not enabled on the old moodle. Try turning that setting off while you restore your courses.