Hello there.
A couple of people have told me of this problem, and there's not much I can do to resolve it.
The plugin doesn't do anything fancy with video playback, it just uses the built in function from rpgmaker to play them, so any problems with playback it has (low framerate, sound issues, etc) are coming from the engine itself, not the plugin. I might maybe be able to mitigate this specific problem by only allowing the videos to be skipped after a certain number of frames, and maybe that'll give the garbage collection functions time to do their jobs and stop this from happening. But since I'm only using the default engine to play those videos, the problem would still happen any other time a video player.
The best thing I can suggest is to have the final splash video be a very short blank video with no sound (like a couple of frames), so that if it is skipped past and its audio keeps going, it won't have any audio to interfere with the title screen.