The bugs in Mega Man 4, 5, and 6 are expected and I'm working on that. I've even started rebuilding a Mega Man 5 profile from scratch but so far it seems that I don't have solutions. The Panic Restaurant bug is new to me as this is one I haven't had previous issues with until now. I'll look into it.
Being that my own machine is under-powered and likely its graphics hardware isn't all that good, I've come to expect my larger profiles to act up and anyone with computers with a certain spec cut-off experience the same. Until I get this issue worked out, I don't have any solutions how to fix this.
It's likely the 3DSen engine itself has a limit when it comes to certain mappers or the size of the games themselves. I don't know for sure, I don't have a way to diagnose the emulator itself.