Emulator

we do not see on the screenshot it's proof

So checking the box for "Vsync" fixes it? That's not a bug, vsync's optional for a reason. Pretty much every PC game has vsync as an option that you can enable or disable. Without vsync, things run faster but you get screen tearing and other visual artifacts. With vsync, your GPU does a few simple tricks to make sure it only pushes whole frames to the screen, but these tricks include waiting for things, which pretty much always slows things down.

The only reason it doesn't show up when you're in windowed mode or borderless fullscreen (which were the only two ways you could run Dolphin before 4.0-2543) is because Windows (and OS X, and most Linux window managers) does compositing, which means it's forcing vsync on everything to make sure it gets whole frames from every application. For Dolphin, though, it tends to skip a few frames here and there and slow everything down a tiny bit, so we now have exclusive fullscreen to get around that.

Also, those .dtm files you've been uploading for all your issues aren't actually video files or whatever you expect them to be – they're input recordings (e.g. button input) and are entirely useless in this context. (They're really special-purpose and require a lot of setup just to play back, let alone to record in a way that actually allows for correct playback to be possible.) If you wanted to record a video, you could've used Movie > Dump Frames, but even that wouldn't record this specific issue.