Lol, sorry about that. I'm kind of new to all this Mac stuff as well.
Virtual box is like VM Ware where it allows you to run another "virtual machine" inside the Mac environment. Think of it like having another window open where it runs MS Windows 7/8/10/XP where you can easily switch, say, between Safari and whatever windows program you are using. However, by being a virtual machine, whatever happens on that machine stays on it and won't, like if the windows gets a virus and rather than trying to use an antivirus, you can destroy the machine and restart a new one without affecting your Mac. You can also set up Linux to run within your Mac if you are incline to do so. But from what I know, Mac OS is a variant of Linux/Unix anyway. Its a way of "dual booting" but having to be able to run both OS at the same time.
Xcode is a software development kit that Apple provides to allow you to make apps for iPhone, watch, Apple TV, and Macs.
Avira is an anti-virus program just like Norton's, McAfee, etc.
Its possible that you may have programs that run in the background like an antivirus that is causing this issue and its conflicting with the new El Capitan update. I'm running the same 10.11.5 version and have not have to issue recur.
I remember when I had the issue, what I did was wipe my drive clean and reinstall (be very careful not to wipe out the recovery partition, which I did once.) and slowly reinstall each program to find the culprit and it was a new version of virtual box. I then went back to an older version and didn't have any issues. I am currently running a newer new version of virtual box and have not had any issues.
With that said, there was someone that mentioned it was a hardware issue when they brought it back to the Apple store.