We use VLC for our access cable tv station playback. Video files are run via applescript, and it runs 24/7. We use a Matrox Convert DVI to create a 1600x1200 external monitor, and VLC is set to Fullscreen there, with video settings at Fullscreen, Float on Top, and Locked Aspect Ratio. The Matrox converts that back to 720x480 for cablecast.
Since 3.0, maybe 5% of the time, a video will appear at Normal Size, which means it only fills about a quarter of the screen. It doesn't seem to be related to anything about the video itself -- the same video that showed at Fullscreen one time will display at Normal Size the next.
I've been searching through the forums, and I can't find anybody else mentioning this problem. I'm currently running VLC 3.06 on El Capitan (legacy hardware!)