When I hover the pointer over the progress bar, with the little teensy popup indicating the timestamp...out of nowhere the window manager (lxde)'s task bar shows it as a new window! Like for some reason LXDE thinks it's a full fledged popup dialog. This is a minor regression, as it didn't used to do this in the past. only thing I remmeber chanigng was VLC's version. the title of the "window" in question is just "vlc"
Created attachment 520944 [details] emerge --info
As you've had a similar issue before please try under a different desktop environment.
I had the same sort of issue with a popup menu in the windows steam while running under wine.
Adding lxde as I think there is nothing to do for vlc in this case.
I run stumpwm and have this same issue with >=media-video/vlc-3.0.0. Because stumpwm is a tiling window manager, once the popup registers as a new window it ends up expanding to fill the whole frame vlc is running in. This makes vlc 3+ pretty much unusable on my system if I ever want to seek during playback.
Fixed for me in 3.0.4. Did not try earlier versions.