Could you please be a little more specific, and/or share the code?
I simply meant what I said... There's a register that reflects the CRT's status (electron beam position, blanking...) that the games depend on to avoid graphics glitches. It's undocumented, and needs to be emulated correctly or you run into various problems.
Also, when forced interleave between the CPUs affects the timing, it's time to get rid of it, and just sync the CPUs whenever they access a shared resource, which is how things generally *should* work anyway... batrider and battle bakraid seem to let the Z80 trigger interrupts on the 68K as well as the other way around, so you can't get it perfect unless you have per-instruction interleave, but you can get close enough.
I did both of the above for batrider and battle garegga (battle bakraid aways had proper cpu sync), and the games run a bit better. I'll do the same for the rest when I have time.