Yes, the new GAL removes the input for the jumper. What I guess is happening is that the input is not correctly pulled up, and the game randomly switches between the top and bottom half of the EPROM. For Espgaluda it crashes as soon as it happens, as the second half is just $FFFF, for Ketsui it crashes as soon as there is a difference between Normal and Trap. If you have a scope you could trace the highest address line for noise.
I double checked the data sheet, and it doesn't look like the pull up is a programmable option that could be different depending on which programmer you use. You could verify the voltage across the GAL, in case it drops too much as system load increases. Though I expect you've got a better power supply than me, and voltage drops would probably cause bigger problems. I don't think it is a GAL quality or "fake chip" problem either if you bought from Digikey.
If you want the jumper to work you could try the pull-up resistor mentioned above. Otherwise, does anyone who has done this for longer have any idea? If the external pull up resistors work I can integrate them into the layout, so people can populate them if necessary.
The Trap version of Ketsui uses exactly the same sound EPROMs, and the bus configuration doesn't change. I assume you tried cleaning contacts, wiggle the cartridge?