Emulator

Game Name?
All games

Game ID? (right click the game in the game list, Properties, Info tab)
All games

MD5 Hash? (right click the game in the game list, Properties, Verify tab, Verify Integrity button)
All games

What's the problem? Describe what went wrong.
Hotkeys stored in Hotkeys.ini works well in game launched with dolphin-emu but not when launched with dolphin-emu-cli (nogui version).

What steps will reproduce the problem?
Hotkeys works: dolphin-emu Resident\ Evil\ 4\ (PAL).gcz
Hotkeys not work: dolphin-emu-cli Resident\ Evil\ 4\ (PAL).gcz
dolphin-emu r9958 compiled from AUR in Arch Linux.

Is the issue present in the latest stable version?
Last stable version is too old :)

If the issue isn't present in the latest stable version, which is the first broken version? (You can find the first broken version by bisecting. Windows users can use the tool https://forums.dolphin-emu.org/Thread-green-notice-development-thread-unofficial-dolphin-bisection-tool-for-finding-broken-builds and anyone who is building Dolphin on their own can use git bisect.)
Not applicable.

If your issue is a graphical issue, please attach screenshots and record a three frame fifolog of the issue if possible. Screenshots showing what it is supposed to look like from either console or older builds of Dolphin will help too. For more information on how to use the fifoplayer, please check here: https://wiki.dolphin-emu.org/index.php?title=FifoPlayer
Not applicable.

What are your PC specifications? (CPU, GPU, Operating System, more)
i5 with NVidia 840M over ArchLinux

Is there anything else that can help developers narrow down the issue? (e.g. logs, screenshots,
configuration files, savefiles, savestates)
I whish can be reproduced.