SIRJAMES  I had to manually uninstall the program. I started to have shut down problems on two of the computers i was using and been trying to fix the issue and last night i check the activity monitor to see what i could find as the problem. I no longer use little snitch and uses app zap to uninstall the app and noticed that there was a little snitch file that was running so i tried to quite it, it would not quiet so i forced quiet it and it still would not quiet. I i looks at the inspect window and found all the hidden little snitch files (one in the library at the root level and one in your user folder, once i deleted them and restarted the computer and then emptied trash and then verified the program was not running. I gather the program was not shutting down properly when I would shut down the computer. Word of advice if u start to have shut down issues try totally uninstalling the app and see if your problems are fixed. When u delete the files only delete the ones that actually say little snitch - because the program does seem to attach to other core services of your mac (most of which i noticed are the same apps i am having problems repairing permissions on). I think the program does a little more than a firewall - kinda believe it is a mailware program. Maybe the problem was fixed in the newest version but i would never use it again. If others are having the same issues try manually deleting all the files and see it that fixes your issues.   
(Version 2.2)