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I know this isn't the right forum, but I cannot find anywhere more pertinent, since I don't have a Windows computer from which to make a problem report.
I upgraded from OS X 10.10 to 10.11 yesterday. When I plug in my MS Natural Keyboard 4000 today, the Windows and Alt keys are no longer swapped. I looked in the Microsoft Keyboard area of the System Preferences. Keyboard Info says no MS keyboard has been detected. I reinstalled the drivers from Microsoft-Desktop_d305.dmg, which annoyingly requires a System Restart. That made no difference.
To be clear, the keyboard is working. I'm typing this report on it. However, it's not being detected as a Microsoft Keyboard and so the Windows and Alt keys are not being swapped. I'm having to fight my muscle memory to get things done, since I expect to find the Cmd key immediately to the left of the space bar.
The keyboard is plugged directly into a USB port on my MacBook. However, when I first plugged the keyboard in after upgrading to OS X 10.11, it was into a USB hub.
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Locked Question. This question was migrated from the Microsoft Support Community. You can vote on whether it's helpful, but you can't add comments or replies or follow the question.
Someone suggested that I go into System Preferences > Keyboard > Modifier Keys. I swapped the Option and Command keys and now I'm much happier.
According to the response I got in https://discussions.apple.com/message/29052150?ac\_cid=op123456#29052150
Due to the security changes in El Capitan, the MS Intellitype drivers don't work. There is no workaround. MS is finally going to have to update the software, which hasn't changed since Lion's release.
You'll notice almost none of the special keys work, either.
For the moment, the best solution I've found is:
https://pqrs.org/osx/karabiner/
It is not perfect, but it remapped everything I need - most importantly being the Windows key and Alt keys.
The above fixes that issue, but the number keypad still did not work.
So this took care of that problem. All the functionality I need for audio post work is restored.
Hope this helps you.
I'm using MS Desktop 3000 and I also became angry when I noticed that it was not compatible with El Capitan. But I found the solution. I switched to a 3rd party software. Try USB Overdrive http://www.usboverdrive.com/. It's a shareware and is free forever. The only limitation is a popup notifcation to upgrade when you start your computer.
I havent upgraded yet but it's something that I will consider if MS didn't solve the issue.
And the good thing about USB Overdrive is that.. it was able to customize buttons that IntelliType didn't allow me to.. For example, now I can customize Number Lock Key (on the number keypad), Insert Button, and everything else. The only problem is.. it was not able to detect 5 special hotkeys. Otherwise, it's just perfect.
Good luck!
You may post your query in the Apple forum.