I could not open the experiment linked above (perhaps it is not publicly accessible). So, I could not observe the problem for myself.
The cause of the problem might be the choice of units in the experimental settings. It is also possible to change this for each movie component of the experiment, where pixels is often a good choice. It is usually best to leave the global preference as height to make text sizing easier.
Assuming that you have resized all of your movie files to their intended display size (in pixels), then you can safely leave the Size field of each movie component blank, so that the actual size is used by default. The same applies to the Position field, if you intend the movie to be centred on the screen.