I am on the most recent MacOS: v10.12.1, with the most recent Karabiner-Elements: v0.90.61.
I have keyboard repeat at a very fast rate (in System Preferences). If I turn on Karabiner, it prevents the keyboard repeat from working well. It will only repeat 3-15 times, then stop, then I have to lift up the key and press it again. You can see that here: http://cloud.3rdMillWeb.com/1X2P0W2s3R1y.
And here you can see how keyboard repeat works when I Quit Karabiner-Elements: http://cloud.3rdMillWeb.com/1p0O3W1T0x11
Could you confirm the latest version (v0.90.63)?
@takezo I also have a similar problem with v0.90.64 on Mac OS X Sierra. I used this configuration:

In my case, the key repeat completely stops working even after quitting Karabinar-elements. And the key repeat configuration in the system preference showed weird values:

It seems Karabinar's key repeat setting happened to affect the disabled keyboard configuration:

If I turn on 'Modify events from this device', the key repeat settings are working as expected.
Sorry, I missed this somehow. A recent update fixed it. It is now just managed in System Preferences.
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@takezo I also have a similar problem with v0.90.64 on Mac OS X Sierra. I used this configuration:

In my case, the key repeat completely stops working even after quitting Karabinar-elements. And the key repeat configuration in the system preference showed weird values:

It seems Karabinar's key repeat setting happened to affect the disabled keyboard configuration:

If I turn on 'Modify events from this device', the key repeat settings are working as expected.