I found some broken dip switches:
galaga - setting it to freeplay breaks the game and it no longer loads past "ROM OK"
toaplan GP9001 hardware, toaplan-developed games (batsugun, batsugunsp, dogyuun, truxton2, possibly others, but not Raizing games on the same hardware) - region cannot be changed from the default (Korea for Batsugun, Japan for others), changes have no effect.
Setting these dips seems to work ok in MAME.