Blender Version: Tested with blender 2.8, but all versions. Ancient bug.
When you cut a video strip with a speed controll video strip, the newly generated strip doesn't start from the frame where it should.
When loading the .blend you only have to execute one cut, with K or Shift+K and you can see in the preview panel, above, that the execution jumps and should not.
You must select both strips, the video and the speed control.
I have also noticed that if before creating the cut, you convert the two strips into a meta strip, this error does not occur.