Well, problem solved. And it did not require "blackout" or "sleep" or anything.
In MSDOS.SYS, under options, add the following: LOGO=0
This disables the boot screen entirely. Now my system boots right to GL with no side-effects. YESSS!
So I spent most of yesterday going through my game lists, finding the ones that don't work and also marking each one as Vertical or Horizontal. WOW what a pain. I had already created these lists by genre using, umm, using some list maker. Weird thing is, some working games got left out completely. I don't understand why. I'm going to have to hunt through and find all the ones not in any lists. YEOW!
