In system preferences i set F-Keys as regular function keys (which is only shown if i connect my BT Apple Keyboard). But since last update (0.90.58) Karabiner-Elements ignore this setting. In Karabiner-Elements i modified "scroll lock" to "Fn-Key". With 0.90.58 i have regular function Keys only if i press my binded Fn-Key. If i go back to 0.90.55 it's working normal.
If you are using keyboard-and-mouse combined device, Karabiner-Elements ignore them in default.
Please check Devices tab in Preferences.
@tekezo what you are saying is to uncheck "apple internal keyboard / trackpad" in devices?
In that case the system stops to see my capslock remap (I've remapped it as f18).
If I do check "apple internal keyboard / trackpad" in devices, then all my functional keys start to work according "functional keys" in karabiner tab... Unfortunately in this case fn+Fkeys combination cease to work properly.
So what I'm saying is that "functional keys" from karabiner-elements and system setting "keyboard -> Use all F1, F2, etc. keys as standard function keys" are conflicting with each other.
Confirmed. I don't need remap F* keys. In past versions all works as expected. But now they are not removable through GUI. I found workaround: "fn_function_keys" : {}, in ~/.karabiner.d/configuration/karabiner.json.
My standard setup is simple, I just remap caps-lock to esc and that's it.
I use system preferences -> keyboard -> Use all F1, F2, etc. keys as standard function keys.

I don't want karabiner to do anything with my function keys but karabiner still overrides the function keys by default to be the mac special keys.
If I remap the function keys in karabiner to the corresponding function keys returns the function keys to their normal mapping HOWEVER the fn key has no effect and, for example, I cannot press fn + f10 to mute sound. This was working in the previous version.

@tekezo I don't want to simply turn off karabiner for an input device because I still want it to remap keys in Simple Modifications. I do not want karabiner to do anything with the Function Keys which it seems impossible to do. I want to still use the fn modifier combo but it appears that karabiner overrides the command not allowing fn + F# key combo to work.
@akaspin This returns the function keys to their default state however I still cannot get the fn modifier combo to work with karabiner applied.
@digitaldreamer BTW, latest release of macOS 10.12.1 allow to map caps lock to esc without external tools :)
@kron4eg nice! I'll take a look, seems like a simpler option overall. Thanks for the heads up.
UPDATE: confirmed
@digitaldreamer Like this: 
But away from this special case (since in resolved by OS), your point is totally valid, karabiner started to interference with function keys and doesn't take Fn button into account :(
@kron4eg
Yes, for my use-case it appears I do not need karabiner. However, I feel the fn button interference is an issue other people would be interested in solving. Thanks!
On my system, this functionality was working correctly until I installed updates this morning:
I did a quick glance over the diff between 0.90.53 and 0.90.58 and I didn't see anything that looked related to this issue, so my suspicion is that the regression was caused by the macOS update.
Using built-in trackpad on a MacBook Pro, no external devices connected.
Thank you for feedback!
Karabiner-Elements v0.90.58 has an issue that ignores "Use all F1, F2, etc. keys as standard function keys" setting in System Preferences.
I've fixed this issue in v0.90.59.
Please upgrade to the latest version.
Then restore your Function Keys setting to the default and use "Use all F1, F2, etc. keys as standard function keys" setting in System Preferences.
Confirmed fixed in 0.90.59.
@tekezo thank you very much! works as expected now 馃憤
Most helpful comment
Thank you for feedback!
Karabiner-Elements v0.90.58 has an issue that ignores "Use all F1, F2, etc. keys as standard function keys" setting in System Preferences.
I've fixed this issue in v0.90.59.
Please upgrade to the latest version.
Then restore your Function Keys setting to the default and use "Use all F1, F2, etc. keys as standard function keys" setting in System Preferences.