Ah yes, I see now! Thank you! The linked post from zeroone didn't make sense to me at first. I'm like "PRG-RAM write protection? Who cares? What relevancy does this have?", but then I scrolled up in the referenced thread and realised it's extremely relevant.
To explain: I'm always suspicious of prototype or "development ROMs" etc.. They're often coveted by people who spent stupid sums of money to get them, usually can't guarantee a proper dump of the ROM (so corruption there is possible), and often won't help with ensuring such a cart make it into the hands of someone who can do the proper RE so that it can be dumped + emulated properly... yet they release what they have into the wild and people say "it doesn't work right!" when for all they know it doesn't work right on real hardware either (because coveting collectors/hoarders refuse to assist in the process). It's even more complicated when the game uses a still-not-quite-fully-understood mapper like MMC5. (Ys 3 on NES was another example, back in the late 90s during the emulation peak, and I was part of that. It's a cart I own that was weird/interesting in some of the PPU stuff it did. I suspected for a long time it was a PCB with a unique set of PPU address line traces, but that got refuted, I think.)
Anyway, yeah, it sounds like this is going to require emulator code changes. Can you submit
a GitHub Issues request for NestopiaUE discussing this problem + what needs to be done? If not, I can try to do the submission, but may need zeroone's help. I might have to spend time in Mesen and getting familiar with MMC5 (the latter I try to avoid as much as possible, haha).
We also need to have a clear/concise bullet list of what emulators (and their versions, as well as platform (ex. Linux vs. OS X vs. Windows -- yes this matters!)) experience the problem so that reports can be submit to each appropriate author/team. As it stands now, it sounds like some version of FCEUltra (is that FCEUX? Or are you using the older FCEUXSP? Etc. etc. -- too many forks!) doesn't work, some version of Nestopia doesn't work, and some version of Nintaco doesn't work. "And others" is not particularly helpful if we want to have this emulation problem fixed.
A good example would look like this (AND THIS IS ONLY AN EXAMPLE):
* NestopiaUE v1.49, Win32 -- corrupted graphics during {whatever}
* FCEUX 2.2.3, Win32 -- bulldozing causes my PC to catch fire and stabs my dog
* FCEUX SVN xxxxxxxx, Win32 -- works
* Mesen DevWin 0.9.7.92, Win64 -- works
* NintendulatorDX v35, Win32 -- corrupted graphics during {whatever}
* Nemulator 4.2, Win32 -- works
etc... you get the idea.
From what I am reading, I am only seeing one solution which is to remove read protection from PRG RAM, correct? What is the other?
I'm 2 for 2 today when it comes to missing things. 
