"Don't get confused by the fact that some of us are talking about Parallels. Parallels is NOT the problem.
Problems arise when some "orphaned" files remain in the above mentioned folders, after removing an application... in my case, for example, there were some files left from Parallels and other files from another application: I had to remove all of them to solve, not just those related to Parallels."
+1 Sorry for the stupid misquote/reply mechanism. This site absolutely blows monkey turds. (It is slower than molasses and has long outstanding login anomalies.)
I use parallels and have this issue. I found that I had installed and then uninstalled a Verizon USB hotspot driver. The uninstall left a plist in the aforementioned folders. I deleted the plist, and shutdown times are back to normal.
For anyone having issues, scan through the plist files and if you see one that is a program that you uninstalled, remove the plist and see if that helps.