I just updated the subject, because the dongle is obvious not broken.
Not a huge help, but confirm the same issue here and updating the eLicenser version currently makes no difference at all.
My solution was the boring one in terms of lost productivity and rolled back via time machine and this fixed the issue. There were also various parts of my system that refused to see other USB items such as extra drives that worked with no issue before.
I was on 10.11.3 and attempted the upgrade to 10.11.4 with the results above. As a tester on these things this has been reported to Apple through their feedback system, hopefully to be read 
There is obviously nothing wrong with the dongles in my opinion, just the ability to see/read them correctly via the latest updates.
I believe you are right DaveP. It looks like a USB issue in El Capitan, i didnt have the soundcard issue in Yosemite, and certainly not the dongle issue.
I do have back up, but i am not fond of rolling back. I am affraid it will do more damage than now?!
And I wonder when Steinberg are visiting this thread, like Dirk did with the others?
Apple does appreciate your feedback.
In fact, they got in touch with us to discuss certain USB related issues that became apparent with the latest beta seed of OS X 10.11.4.
From what I’ve learned, I’m confident that the final version of OS X 10.11.4 will not suffer from the issues that forced you to roll back to OS X 10.11.3.
Personally, I have not been able to find any USB-eLicenser that didn’t work on any of my OS X 10.11 ‘El Capitan’ installations.
As I’m aware that there are now several customers like you that cannot use their USB-eLicenser anymore after upgrading to El Capitan, it is frustrating not to be able to reproduce/test/investigate the issue on any of our machines yet (which indicates that you’re hitting a rare incompatibility).
On the other hand, we’ve already discovered other irregularities regarding El Capitan’s USB stack, and Apple is currently investigating them as well.
Until we receive further information from Apple, I would advice to roll-back to OS X 10.10.5 in case you encounter difficulties using the USB-eLicenser on OS X 10.11.
If your USB-eLicenser works fine on OS X 10.11 ‘El Capitan’, there is no reason to roll back.
Folks,
I’m suffering the same predicament and having an absolute nightmare.
I posted a fresh topic about this and it seems to be Apple that need to work on a fix.
I too updated my USB-eLicencer after I got the Steinberg “no licence found” message but it made no difference. Really upsetting as I have a few deadlines to work to. I emailed Steinberg a few days ago but had no response yet but I expect they will be extremely busy.
Has there been any further solutions found ?
Definitely something wrong but maybe, someone can do something with the following:
I’m using eLicenser Control Center version 2.6.0.0 on Mac Pro and MacBook Pro, El Capitan 10.11.3 and Cubase 8.5.
Till now, No problems.
I also did a complete clean install on a spare drive to check-it (the only drive in my mac at the moment of testing)
Also all fine.
Good-luck!
I’m very sorry, but this does not seem to be a very rare problem. I have the same issue here with the eLicenser stick on a Macbook Pro and iMac both running with El Capitan 10.10.4 and Cubase 8 and 8.5.! After reading this thread I’m not very optimistic that there might be a quick solution. Though I’m new to this forum, I’ve been working with Cubase since the 90s on my Atari and most of the times it has been very reliable. But this situation leaves me quite helpless. I think Cubase is no longer very usable on a Mac and Logic might be the better solution.
Version 2.6.0.0 ? As far as I know, the newest is: 6.9.2.1183 - Did your type wrong, or am I missing something? 
Yes, they seem to be very busy, it takes up to 14 days for me to get a reply, in the mail correspodence I have with Steinberg regarding this.
This situation is surely a pain in the beep !
I’m using version 6.9.2.1183 on El Capitan, no issues.
unfortunately rolling back to 10.10.5 is not an option for me. I guess I just have to wait for 10.11.4 or even later. I raised this issue over several weeks with Sternberg’s support people in australia. Al they can tell me is that they are still waiting to hear from Sternberg, and that it must be my individual machine…
Just to clarify about the version confusion:
The eLicenser Control (eLC) software package consist of several components (drivers, DLLs, etc.) which each have their individual version numbers.
The most visible component is the eLicenser Control Center (eLCC), being the GUI component of the eLicenser Control software package.
So, the eLC version number is something like an overall version number and should be used to refer to a specific setup. The eLC version number is displayed most prominently in eLCC’s main window title bar.
Also, you can open eLCC’s “About eLicenser Control” info box to view the version numbers of all eLC components.
Update:
I reinstalled 10.11.2 though the App Store. Now the eLicenser is working.
Well that is great JueB!
Is it possible to downgrade from 10.11.3 to 10.11.2 ? Which version did you run before?
I know this won’t help anyone but I just want to report this is happening to me as well, even though my MacBook Pro which has the same OS as the iMac, still reads the USB dongle ok, my main production iMac does not.
Running El Capitan 10.11.4 Beta (15E33e), this is the second Beta and I updated a two days ago to no avail.
eLicenser version: 6.9.2.1183.
Similar issue with me. USB-eLicenser gets recognized for a very short time and then it can’t be read anymore unless I disconnect it and reconnect it again.
Try to “Exit/Close” any “third-party” application on your Mac.
I installed the Duet Display app last week. Now if i close the app, the e-liscenser poop can be read.
And by the way, STEINBERG, it’s 2016. Having to register on a freaking forum when i’m already a Steinberg Registered customer, it’s F******* annoying and you are the last company of your kind. Update your freaking system.
Steinberg, why are you telling people their dongles are broken??? This is so annoying why you would misdiagnose problems that people are having?
i had this very same issue when I updated to 10.11.3…NONE of my elicenser related software would run.
Luckily, I rolled back to 10.11.2 and it instantly fixed the problem. The very next day Apple released 10.11.3 and of course pulled 10.11.2 so people can’t download that anymore.
But rest assured people this is a software related issue.