Artie, with the additional system tweaks that you run (Little Snitch, et al) you may be seeing a symptom of a conflict with one of those add-ons being a contributing factor. Next time this one surfaces, try starting in Safe Boot mode to lock out third party add-ons and let us know what that does for you.
FWIW, my 10.11.2 El Capitan install has been without any challenges and without system add-ons.
