NutritiousMusic: I've been hitting a similar issue and I think I've figured out a solution for it.
Go to the WC3 install folder and double click Launch Settings. This will open the games video, sound, & controls configuration menu. Do the joystick calibration and video tests as normal. When it goes to the SVGA test, if you've having this issue, you should see text on the top and bottom of screen briefly, before the screen adjusts so that you only see the top text. Apparently, this is some sort of test to see if your system could handle the old SVGA video mode. In case you didn't see it before it changed, there is text near the bottom of the screen that says something to the effect of hit Y if you are seeing this text to use an alternate SVGA mode.
Press Y on that screen. Go through the rest of the music, sound effects, and controller setup menu if you like (all my music and sfx tested out ok on default settings and the only thing I changed was to use a joystick by default). Then go to Save Settings And Exit.
Upon launching the game, you should no longer have the pauses before each in-game video screen.