I installed Karabiner Elements 0.91.6 through Homebrew to see if I could turn the menu key on my external Microsoft keyboard into something functional for Emacs. When I did that, though, I noticed that Command-Tab and pasting with keyboard shortcuts didn't work. I suspect the alt-to-command mapping is globally disabled, but I didn't verify all the possible shortcuts.
I have the same issue and the same keyboard. Did you find a solution @ceridwen ?
Sadly, no, I haven't. I've tried a couple of times, the problem's still there last I checked, and I haven't been able to work around it.
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Last I checked, this problem still exists, unfortunately.
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.
@ceridwen so did you have Command and Option defined in System Preferences -> Keyboard -> Modifier Keys?
If so Karabiner disables those mappings, as it can't work with them (it's in "Limitations" in the docs). You can get exactly the same result though by just doing the same mappings in karabiner elements, e.g.

It's possible, it's been several months since I last tried it. I will check again at some point, but not right now.
I have the very same issue and suggestion above doesn't work. Furthermore, when I try to copy/paste keyboard types special characters instead. And this is for every key combination.
@soberman does Cmd-c print ç and Cmd-v print √? If so that means your Cmd key is actually an Option key.
You can check by running Karabiner-Eventviewer and seeing which keypresses are registered for each key (left_gui is Cmd and left_alt is Option):

If doing the modifications I suggested in https://github.com/tekezo/Karabiner-Elements/issues/823#issuecomment-388561395 doesn't work, can you post a screenshot matching the one in that comment?
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.
This issue is still valid. I just updated from a previous version, and copy/paste broke immediately. Is there no attempt to retain previous settings between versions?
Here's a screenshot of the interface shown in #823 (I tried to copy/paste the link, but I can't becasue copy/paste is broken. sad trombone)

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I have the very same issue and suggestion above doesn't work. Furthermore, when I try to copy/paste keyboard types special characters instead. And this is for every key combination.