You are not alone. I have been plagued with that since the first El Capitan beta. I reported it to Apple through the beta test system and they suggested turning off, getting rid of Shockwave and/or Flash — it did not help. I switched the backup drive from a Time Capsule to an attached drive and no help there. I have the same results when logged onto another account so the problem is systematic, but I have yet to figure out what the stopper is.
