Cause

The problem is that seeking video (by setting it’s currentTime) is asynchronous.

You need to listen to the seeked event or else it will risk take the actual current frame which is likely your old value.

As it is asynchronous you must not use the setInterval() as it is asynchronous too and you will not be able to properly synchronize when the next frame is seeked to. There is no need to use setInterval() as we will utilize the seeked event instead which will keep everything is sync.

Solution

By re-writing the code a little you can use the seeked event to go through the video to capture the correct frame as this event ensures us that we are actually at the frame we requested by setting the currentTime property.

Example

// global or parent scope of handlers
var video = document.getElementById("video"); // added for clarity: this is needed
var i = 0;

video.addEventListener('loadeddata', function() {
    this.currentTime = i;
});

Add this event handler to the party:

video.addEventListener('seeked', function() {

  // now video has seeked and current frames will show
  // at the time as we expect
  generateThumbnail(i);

  // when frame is captured, increase here by 5 seconds
  i += 5;

  // if we are not past end, seek to next interval
  if (i <= this.duration) {
    // this will trigger another seeked event
    this.currentTime = i;
  }
  else {
    // Done!, next action
  }
});