I think you are going to have to ask David Dribin.
I haven't run into those kinds of problems on my machine yet. My machine is running in win95 DOS mode.
I use batch files instead of letting GL directly launch the games. You might want to give it a try, because you could set different options for each game as needed.
Here is an example of one of my .bat files.
CD C:\MAME
IPACUTIL IP_MAME.CFG /B /S
MAME GALAXIAN
IPACUTIL IP_GL.CFG /B /S