Hi Holly-
When you make settings changes on the lab account, they don't apply to existing labs that were previously created. The settings only apply to new labs that are created after that point. Can you check to see if you create a new lab, that the auto-shutdown settings are then applied?
Also, a VM does still incur charges if you shutdown the machine using the Start menu from within the OS. To ensure that a VM is shutdown properly so that it doesn't incur charges, students will need to use the Start\Stop toggle button. In addition, we also recommend using quotas, schedules, and the auto-shutdown settings to help ensure VMs aren't left running unexpectedly.
We also have an article that shows how you can disable the shutdown option on the Start menu to make this less likely to be used by students:
https://docs.microsoft.com/en-us/azure/lab-services/how-to-windows-shutdown.
Note that the product team is currently working on the upcoming public preview for Azure Labs - one of the key aspect of this is that they've made big improvements to the reliability and performance of the auto-shutdown experience for lab VMs. Included with this, is that by default, when the OS shuts down, the VM will also be shutdown so that costs are no longer incurred.
Hope this helps.
~Nicole