Disappearing Safari Extensions, Other App Settings, Etc.

I have a MacBookPro that is 1.5 years old and sometime last year I started having issues where while working Safari extensions would just disappear. They are there and then during the course of the day they are gone. I've seen this pattern as well where you reboot and they may then come back and then the next time you reboot they go away.

Similarly, many other settings keep disappearing. Apps that are set to start on login may or may not do so. You check application preferences and where they have an option to start on login that is now unchecked even though they were set to do so before. And there are other issues similar where certain settings just don't stick.

During the holidays I reformatted the drive and installed the OS from scratch. Everything was reinstalled, I did not restore from a backup. And the same things are happening again. One thing to note is that before wiping everything clean I could see permission errors in some folders and in particular where Safari extensions are stored. Nothing I did would fix that problem. And, I used the on boot ability to do a disk scan and did get an error that at the moment I can't recall what it was. At this point the disk tests as okay and I've not seen any permission issues but this type of problem still exists.

Other than going to an Apple store I'm at a loss for what to do. I've very technical so I have no problem doing more investigation but just not sure what is next... I'm due for a new MacBook Pro in 5 months so I may just wait it out.