Are you manually launching DisplayFusion, or do you have it set to run at Windows startup?

Ok, if you create a shortcut for DisplayFusionCommand.exe instead, and add the -monitorprofileload "profilename" parameter, that shortcut will launch DisplayFusion and apply the Monitor Profile.

Steps on how to do that can be found here (skip the last 3): http://www.displayfusion.com/KB/LoadMonitorProfileOnStartup/

Hope that helps!