ShaddamIV wrote: I'm using PrefSetter to edit my prefs. Interestingly, the array seems empty:
Should I perhaps delete the plist file? Or do you perhaps know what should be in it?
I'd only use Pref Setter to read a .plist and not use it to write to it because it's old software and actually doesn't handle all .plist file properly! 
So I personally use Xcode or defaults.
In a Terminal use the following command syntax to set a Virtual Machine in the powerOnAtStartup.cfg array.
defaults write com.vmware.fusion.plist powerOnAtStartup.cfg -array "$Fully_Quilified_Pathname_of_the_.vmx_configuration_file"
Using the Virtual Machine from the previous post the command would be as follows:
defaults write com.vmware.fusion.plist powerOnAtStartup.cfg -array "/Volumes/HFS+/Virtual Machines/VMware Fusion 6.0.2/Apple/0S X 10.9 Mavericks/OS X 10.9 Mavericks.vmwarevm/OS X 10.9 Mavericks.vmx"