I finally found the answer. The Profile Manager is part of WDM but enabling/disabling it wasn't intuitive to me. For anyone else with the same issue the answer is in the Admin Guide. As a shortcut to the answer here's a screenshot of where to find the setting. [IMAGE] 
I'm upgrading from 5.0 to 5.5 on Server 2012 R2 but the install aborts with the error "Please disable Profile Manager before upgrade".  I have no idea as to what 'Profile Manager' this is referring. I there are no tasks or services by this name and the 5.5 install guide does not appear to mention a Profile Manager. This is probably going to be a face-palm situation when someone points out the obvious answer but I'm currently at a loss. 
Upgrade to 5.5 fails with "Please Disable Profile Manager"