I use CIBC, so I followed the instructions for setting up an account to pay to McMaster to clear off my fees. McMaster University as the payee, and my student number as my account number. I paid off the balance of my fees on August 29. Today I checked my student account and NOTHING HAS CHANGED. I still owe the exact same balance! Should I be worried?!

You might want to call Student Accounts and Cashiers, I don't know if they can tell you anything that you wouldn't have already seen on MUGSI but they're definitely the best bet for help at this point.
http://www.mcmaster.ca/bms/student/index.htm

They usually take a couple business days to process, but never more than a week. Does your bank account statement show the money withdrawn?