So I've encountered this issue on both the GOG and Origin version of Wing Commander 3 when running in fullscreen. Every time I click to another room, the game will display the screen either super squashed or stretched out, hang for a few seconds, then "snap" the screen into the correct resolution. After that, it runs perfectly, correctly displayed in fullscreen.

I've messed with various settings in the DBox config, but nothing seems to fix this problem. If I run the game windowed, then the delay isn't an issue, but I can catch a very quick "squashed to correct" flash on each transition.

I'll add that the gameplay runs fine; this occurs in all the navigation/fmv transitions. I've added 2 pics. The first is what the screen hangs on at the transition, then the second is a few seconds later when it "snaps" in.

this game seems to do a new fullscreen access for each movie and game menu launch.
my geforce drivers take a short time to do this, i have a short flickering/black screen or the same thing as you have.

I try to made a borderless fullscreen windows with Borderless Gaming (github.com/Codeusa/Borderless-Gaming/releases/ ) but the titlebar of the windows don't stay hide for the same reason of the fullscreen problem

I replace dosbox 0.74 (2010) by EmuCR (dosbox svn r4000 10/2016, see EmuCR here : dosbox.com/wiki/SVN_Builds )
problem always present but much more playable (take less time to switch between movie/menu)
And I use the In-game options "transitions" for remove useless movie (open door, close door, walk...)

Have you tried setting the fullscreen resolution of DOSBox to your desktop resolution and using opengl or openglnb as the renderer? This kind of flickering and stretching should only occur if the fullscreen resolution is set to "original".

Thanks for the fine hint! The problem still persists but it switch a lot faster between squashed and correct screen now!