I don't know. I only recall that switching the VGA option sets the screen to 320x240 resolution. SVGA uses 640x480.
To be precise, the vga option makes it render the 3d graphics in 320x240, scale it up to 640x480, and draw the HUD at full resolution. But it's odd that this only stays on for a second and then switches back to the svga mode.
Maybe it detects an abnormally high framerate or something, but it's still odd that it doesn't respect user options..