For your information, in the past, combo updates have been issued starting with the OS X 10.X.2 release, which might occur months after the original release. Anyway, I suggest 'waiting for the combo update' is not the appropriate solution for you. Instead, you could try a clean install of OS X El Capitan. Use this link to open the El Capitan page on the App Store: Get OS X El Capitan. Click the Download button on the El Capitan page. A file named Install OS X El Capitan downloads to your Applications folder. After download is complete, the installer opens automatically. Click Continue and follow the onscreen instructions.
Once, whenever things started going wrong and we didn’t have any better ideas, we would repair permissions. Thanks to El Capitan’s SIP – and the fact that this has not been of much help for some years – that is no longer available. In its place comes applying the latest Combo update.
The theory is simple and fairly sound.
Apple provides two forms of each update to OS X: an incremental, or Delta, version which takes it up a single step, for example from 10.11.3 to 10.11.4, and a combined, or Combo, version which includes all the updates since the last major release, for example from 10.11.0 to 10.11.4. Normally we update using the App Store, which provides the Delta version. If you have a lot of Macs to update, Apple also provides a separate installer disk image which you can download and use for each Mac.
If your Mac has gone step by step up to 10.11.4, there is a chance that somewhere along the line, the update may not have worked perfectly, or some system files have become a bit munged. Applying the latest Combo updater is usually much less disruptive than re-installing the whole of OS X, so it is a good trick to try to solve problems which appear resistant to everything else – and is quickly becoming a universal panacea.
Even with a relatively slow internet connection, it is not too painful or time-consuming: the current 10.11.4 Combo updater is just under 2 GB, and can be far quicker to install than even a single Delta update. You’ll find it here. If you need to locate another Combo updater, just enter the version of OS X which you want to end up with and the word ‘Combo’ in a search of Apple’s Support site, and it should appear at the top of the hits.
Once downloaded, open the disk image to mount it, and run the Installer package. With a Fusion Drive, it should take but a few minutes, then restarts your Mac and puts you straight back into the Finder as you left it, without even having to log in again.
But the job is not quite complete: there are a couple more tasks which you need to do before this refresh update is done. First, you need to open the App Store app and check for updates, in case applying the Combo update has reverted any regular components that came with it. If, for example, there had been an interim update to Safari since that full OS X update, then you would need to re-apply that interim update, which the App Store should do.
There is also the interesting issue of Apple’s XProtect and other security configuration files, which are normally updated silently. Look at the list of updates installed by opening About This Mac, clicking on the System Report… button to open System Information, then selecting the Installations item in the Software list at the left. List the items by Install Date by clicking in that header, and order them from most recent at the top (you may need to click a second time in the Install Date header for that). Until you see a list with those normally silent updates, your Mac is vulnerable.
Download Os X El Capitan 10.11.4 Combo Update
This is because the Combo update reverts XProtect and other configuration files to those which came with that update, not the most recent. To bring that protection up to date, you will now need to force those to be updated, rather than leave your Mac to catch up in its own good time, which may be during the next night.
There are two methods which should force those to be updated: you can open the App Store pane, uncheck the Install system data files and security updates item, switch to another pane, then back to the App Store pane. Turn that item back on, then click on the Check Now button below.
That may not always work. If it does not, open Terminal and enter the following command from an admin user account:sudo softwareupdate --background-critical
press Return, then at the prompt, enter your admin account password. Terminal will then reportsoftwareupdate[1587]: Triggering background check with forced scan (critical and config-data updates only) ...
and in the next couple of minutes, the updates should be downloaded and installed. Check by opening System Information and looking for those updates, which will be more recent than your OS X Combo update.
Note that if you browse the man page for softwareupdate, you will not see this option listed there, but it does work in El Capitan.
El Capitan Mac Upgrade
I hope that applying a Combo update fixes your problems.