Security update 2016-003 10.11.6 issues I'm not sure whether this is a request for a fix, a warning to others, or just a 'did you see this too?'

Mac Pro 4,1 [firmware upgraded to 5,1]
2 x 3.46GHz X5690
Aftermarket Samsung 1TB Evo 840, AMD 7950
All behaving nicely before the update.

App store this morning wanted to update Safari &amp; a new Security update 2016-003 10.11.6
As usual, I let it do its thing &amp; allowed it to go ahead &amp; restart.

After restart I noticed the usual grey screen Apple logo + 'thermometer' rather than ticking through for a few steps then going to my auto-login, instead stared with the thermometer completely full.
It then went to a total light grey screen + [working] mouse cursor... where it stayed until I forcibly shut it down.

Things I tried with no joy...  


NVRAM &amp; SMC resets 
Single user fsck
Verbose boot [couldn't see anything useful]
Safe Boot [same symptoms]  
From TTP eDrive:-
TechTool Pro
DiskWarrior
DiskUtility
all showed no problems
Restored the entire OS from the Recovery Partition... no improvement.


Then some news
Safe boot gave me the opportunity to log to another admin account
which surprisingly had no issues.

I used that account to disable the auto-login &amp; tried again, with many variations.
I ran Onyx &amp; did a lot of cleaning, checking.
I watched Console &amp; Activity Monitor.

From a regular boot, logging to the spare admin account had no issues, logging to my main account I could barely move. The Finder spent an hour trying to draw the contents of the Applications folder, &amp; even then wouldn't launch anything, claiming every app was damaged.
I could switch to the other account &amp; launch the same app with no issues.

Console showed constant crash reports in launchd each time with a new PID
I couldn't find which process coresponded to any given PID as it was changing too fast but it looked like mdworker was also struggling.
I used Activity Monitor from the other account to kill all mdworkers &amp; also spotlight &amp; things settled down - though I couldn't go back to the main account without it starting over.

Eventually I gave up &amp; did a full restore from Time Machine.
Fine. Worked.

I then split the updates &amp; tried again.
Safari update, OK.
Security Update... back to square one.

[fade to black]

I'm now on another Time Machine restore &amp; am not going near that Security Update on any machine in the building until I hear better news from elsewhere.

[I have probably missed 42 steps in my exploratory method, it's been 12+ hours... please ask for clarification - bearing in mind I don't have the console logs as they were wiped with each restore]
(I would add this as a comment, not an answer, but the system won't let me comment.)

I installed Security update 2016-003 on my iMac running OS 10.11.6 (El Capitan) on Dec 13. Since then I have had two kernel panics, one on trying to wake the computer and one today on startup.

The panic on startup occurred with the Apple logo and progress bar still on screen. There was a single line of text at upper left of the screen announcing the panic. No panic report in logs for that one.

Apple diagnostic test says there are no hardware problems, so I strongly suspect the security update is causing these panics.

Update Dec 21: In my case the kernel panics stopped occurring after I updated Little Snitch from 3.6.4 to 3.7.1. Compatibility with Sierra was added at v3.7.0. Perhaps that also provides compatibility with the El Capitan security update 2016-003. Or perhaps it was just the Little Snitch reinstall process that fixed things.