The only setting I can get to save is the "Run as Designer" option, everything else just resets itself as soon as I hit the close button. So, if I want to turn off "Show Initialization Dialog on Startup" for instance, I open the manager, uncheck the box, close it, reopen and it's checked again somehow.
Note that the title bar of the manager reports that I have administrative privileges.
Windows 7 64bit
ArcGIS Advanced 10.2
Workflow Manager 10.2