I'm having an issue with VLC 3.0.0 (currently the latest version available) on Fedora 27, using rpmfusion's packages.
Because I have a 1920x1200 (16:10 aspect) monitor, I'm running VLC with the "Video alignment" preference set to "Top" (align=4 in the vlcrc file) so that the fullscreen controller won't cover any of the video when it's visible, even when viewing 16:9 files.
The problem is, if I'm viewing a playlist of multiple files and have VLC fullscreened, then when VLC advances from one file to the next, the video's alignment changes to the bottom of the screen! (It'd be one thing if it was simply resetting to centered, but it strikes me as extremely odd that it moves clear across the screen from the top to the bottom.)
This occurs whether it advances automatically, or if I skip past the end or hit "N" to advance manually. It doesn't occur unless the video is fullscreened. (For example, Gnome Shell has the ability to snap windows to the left/right half of the screen. If I snap VLC to the left edge and play a playlist, then the video always stays aligned to the top of the window.)
Some things will reset the alignment back to the top. If I exit fullscreen, alignment resets. If the "Do you want to continue playback...?" message comes up at the start of a playlist entry, alignment will return to "Top" when the message disappears.
Other things won't reset the alignment. If I skip forward/backward in the bottom-aligned video, it stays bottom-aligned. If I have a playlist of 3+ files and I advance from the second to the third, it again plays bottom-aligned (whether the second is playing bottom-aligned, or if it's playing top-aligned because I reset it after it started playing bottom-aligned).
I've triggered this bug with the Messages window open and verbosity=1, and nothing there seemed meaningful or unusual . I've tried it with verbosity=2, but that triggered as much logspam as you'd expect, so I've saved the output to disk and haven't gotten through it all yet.
The aspect ratio of the videos doesn't seem to matter. It happens in 16:9 videos, it happens in wider-than-16:9 videos, and it happens when I mix the two in a playlist.