On December 8, 2015 Apple released OS X 10.11.2, along with corresponding incremental and combo updaters. I subsequently proceeded to update four eligible Macs under my jurisdiction. Three of those four updates went smooth as smooth can be. No trouble whatsoever. The fourth? Let me tell you about the trouble I had with that fourth Mac.
I lost nearly all of my Login Items (System Preferences -> Users & Groups -> Login Items). Previously there had been about twelve items in that list. Now, only one or two. Not good.
Minor problem I thought. I new the list of Login Items is in the file ~/Library/Preferences/com.apple.loginitems.plist. I fired up Time Machine, retrieved a recent version of com.apple.loginitems.plist, and copied it into ~/Library/Preferences, keeping another copy handy "just in case."
I restarted my Mac. Good news! All my Login Items were back. Restarted again. Bad News! Nearly all my Login Items were gone again!
[Days of troubleshooting and head banging]
On December 8, 2015 MacPaw released CleanMyDrive 2, a major update to CleanMyDrive, which has been in the Mac App Store in several versions since 2012. CleanMyDrive is a nifty free menubar app that can eject disk volumes during times when the Desktop is not visible or is otherwise inaccessible. It can also clean invisible files from Windows-formatted volumes, which can be useful when those files may no longer be invisible on a different hardware device. Here is a link to AppShopper's page on CleanMyDrive 2: <http://appshopper.com/mac/utilities/cleanmydrive-clean-and-eject-external-drives>.
Why is this important? When CleanMyDrive 2 is allowed to "Launch on system startup," which is its default setting, it somehow causes ~/Library/Preferences/com.apple.loginitems.plist to be mostly obliterated. Not good.
Bottom line: If you have CleanMyDrive version 1.x.x, DON'T UPDATE to version 2.0. Wait for a newer version released LATER THAN December 8, 2015. If you have already updated to CleanMyDrive 2, go to its Preferences and uncheck "Launch on system startup," then rebuild your Login Items, either manually or from a backup.