Similar issues on Everdrive V3, tho using PAL clone with region switches and two compatibility modes. V1.3 doesn't run at all, even with padding to 4090kb rom size, padded V1.2 shows SEGA and CAPCOM logos, then goes into black screen.
Interestingly, there's no such problems with Black Tiger port from the same developer, as it eventually works with a certain switch combination. So, i guess, there's may be a solution for that in the end.