I've had a bit of trouble with a few programs reading huge amounts of data at startup such as Dropbox, Amazon Drive and Adobe CS, but I was very surprised to find this today when my computer was running painfully slow.
As activity monitor wouldn't show open files and ports, I checked all the files Little Snitch and its bits had open using lsof -n | grep Little
and nothing has any significant size. The only thing I've installed lately has been Amazon Drive to back up photos. Could this have anything to do with it?