Emulator

Game Name?
Xenoblade Chronicles, but doesn't matter.

Game ID?
SX4E01, but still doesn't matter.

What's the problem? Describe what went wrong in few words.
Pressing the hotkey for "Increase Frame limit" decreases it.
Pressing the hotkey for "Decrease Frame limit" increases it.

What did you expect to happen instead?
Pressing the hotkey for "Increase frame limit should increase the frame limit.
Pressing the hotkey for "Decrease frame limit should decrease the frame limit.

What steps will reproduce the problem?

1. Define hotkeys for "Increase Frame limit" and "Decrease Frame limit".
2. Use them in-game. You maybe want to use the "Show FPS" feature.

Dolphin 3.5 and 3.5-367 are old versions of Dolphin that have
known issues and bugs, so don't report issues about them and test the
latest Dolphin version first.
Which versions of Dolphin did you test on?
4.0-5416

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
4.0-5400 and older, I assume. I didn't try anything inbetween latest and this one. It was broken either in the update, that added gamepad hotkeys or in one of the "hotkey fixes" updates.

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
OS: Windows 8.1
CPU: Intel(R) Core(TM) i7-4700MQ CPU @ 2.4GHz
GPU: (NVIDIA) GeForce GTX 860M

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
Nope.