Ah...
Generally speaking that is simply a 'con' perpetrated on users by Microsoft to give the 'impression' the desktop [OS] is fully loaded while actually it is not.
What you see with programs such as Fences which by MS's order of process loading sees 3rd party software load AFTER the OS has finished booting fully is the true time it takes to boot Win 8 / 8.1.
Since Fences is a GUI addon to the desktop it gives the impression it has slowed the desktop loading...but it hasn't. [I think I saw a process load time somewhere for Fences of 0.3 seconds which is in all intents and purposes meaningless...a blink of an eye.
If you Google you'll find registry edits to make Win 8 /8.1 load 3rd party proggies sooner [change the timing/sequence] but personally I wouldn't. If MS wants it done in the order it is then so be it....