many prefs changed after "cloning back" a Sandbox to the underlying drive
 

I updated (via "cloning back the underlying drive") from a Sandbox (using Smart Update) and all seemed to go well. I was able to boot from the target (underlying) drive.

After booting from the Sandbox again, I noticed that not all of my login items started up. Looking at ~/library/preferences I noticed that there were at least 30 preference (.plist) files with a modification timestamp of the time the computer was rebooted after the "cloning back" procedure, including com.apple.loginitems.plist and loginwindow.plist.

Using Time Machine, I restored the entire Preferences folder from the TM backup an hour earlier, and all was well.

Any ideas what this might be about?

When you copy back, none of files in your Home folder are copied. At all... so the copy back would have nothing to do with those file changes...

Interesting....so here was my workflow:

1. (I'm booted off of the Sandbox) Copy back Sandbox to Underlying Drive using Smart Backup
2. Boot off of Underlying Drive to make sure things work well. Normal startup, including all of the login items (Yup! It's all good)
3. Boot off of Sandbox. Whoops! Lots of new pref files, including com.apple.loginitems.plist and loginwindow.plist and none of the previous login items load.

Now, I want to very what I think is correct, which is that the Sandbox and the Underlying Drive share the entire User folder via symlinks, so that the the Sandbox version of the user prefs folder is pointing to the Underlying Drive version of the user prefs folder. In other words, one is not a copy of the other but they are the same folder being pointed to via symlinks, right?

I think my next step will be to see if this sequence of steps leading to this end result is reproducible or just one of those odd coincidences.

Thanks for your quick reply, as always.

Those pref files would all be new if you simply restarted your Mac normally, though... remember, your entire Home folder (your entry in /Users) is symlinked. Everything under there isn't touched...

I'm sorry, I'm a bit confused. If I just restarted my Mac "normally," why would these prefs files be new? Aren't they only modified if something (or somebody) modifies them? Surely com.apple.loginitems.plist persists across restarts, no?

Because they're usually modified when the system shuts down and various tasks save their state.

So, that suggests that what may be happening for some reason is that when the Mac shuts down and com.apple.loginitems.plist & loginwindows.plist get written out, one or both somehow got corrupted and thus lost the startup items?

Possibly, but I can't think of any reason why that would be the case...

Well, it must have been a bad coincidence. Today I repeated exactly the steps I took before, and the plist files did NOT get corrupted.

Sounds like it. It's certainly not anything that I've seen (or has been reported before).