El Capitan settings reset after computer restart
I did shutdown my MacBook last night with everything as usual as it can be. But after booting today I had some settings reset: trackpad and mouse tracking speeds, Xcode documentation packages were missing and a few others that I do not recall now. I have read this kind of stuff happened to beta versions of El Capitan. But more frustrating was that when trying to open Facebook in Safari I was presented with a page by MacKeeper citing that I have 3 viruses etc. My guess is the page was some fake site trying to make me pay for MacKeeper but the way it was show was very strange. I cleared of the history and cookies after that and haven't seen it again. Any clues on the problems?
Also I had to install Chrome just to do a thing on a site(gov site) that required Flash and then uninstalled it. Do you think this might be related with the latest exploits in it?