Aah... so that's it. I run my desktop at 1280x960 (need square pixels for design work).
I tried setting both the game and the desktop to 1280x1024. Some of the switching iis now gone -- between each of the FMVs at startup. But I still get to see the windows desktop briefly between each one (that has always happened), and I still get a noticeable mode switch from the last FMV to the main menu (I can hear the tube or relay or whatever it is making it's loud click noise).
Weird? Normal? Fixable? I've always lived with this assuming it's a limitation of DOS games on Windows, with or without Glidos. If there's a way of fixing it completely that would be most excellent!
Sorry to go off topic...