I just started getting used to my new Macbook Pro 16" and have noticed, that PhpStorm doesn't recognize shortcuts any modifier + Function key (F1...F12). It behaves like I pressed a Function key without any modifiers. I quit any other keyboard or automation tools (like BetterTouchTool and Hammerspoon) and turned out the problem disappears when I quit Karabiner. When I open it again, PhpStorm doesn't see Option+F1, Ctrl+F12, etc. If I open IDE settings (Settings - Keymap) and try to assign any shortcut with modifier (one or any combination of Cmd, Ctrl, Option), the IDE sees only Fxx key. The same happens with empty settings (no ~/.config/karabiner folder). I've also tried to add PhpStorm to "always show function keys" in system (System settings - Keyboard - Shortcuts - Function Keys), but behavior is the same.
Another JetBrains product, WebStorm, have same problem. Adobe Photoshop and MS Excel too.
Karabiner-EventViewer shows keys and modifiers correctly regardless running Karabiner. No errors in logs. I see the issue only on MBP 16" with touchbar. On my old MBP 15" with physical keys and same IDE, Karabiner and OS versions everything works perfectly.
MacOS: 10.15.3
Karabiner: 12.9.2 & 12.9.0
PhpStorm: 2019.3.4
WebStorm: 2020.1 EAP
Adobe Photoshop: 21.0.1
Excel: 16.29.1
Hi have the same problem. The checkboxes to use the function key does not have any effect, in the karabiner-settings such as in the system preferences.
I restarted the system, the service (also with killall), installed everything new, but nothing works:
MacOS: 10.15.3
Karabiner: 12.9.2 (beta) & 12.9.0
I just want to disable the special functions on the f-keys.
Same issue. Shift+F6 in IntelliJ IDEA only records F6. Turns out it was Karabiner :(
Nvm, you need to enable the "Touch bar keyboard" here:

Edit: Since people are referring to this comment, I found the original answer to this issue here.
@huylv Thank you very very very much , you are a great man.
need more configuration this https://apple.stackexchange.com/a/363436/380751

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.
Most helpful comment
Same issue. Shift+F6 in IntelliJ IDEA only records F6. Turns out it was Karabiner :(
Nvm, you need to enable the "Touch bar keyboard" here:

Edit: Since people are referring to this comment, I found the original answer to this issue here.