This isn't a hardware question (at least, it isn't yet, but you haven't asked any question specific to the hardware yet). Why have you reposted this here? You already have a thread for this in what looks like the most appropriate section.
If you are trying to report a bug with Nestopia and Nintendulator, you'll need to post a ROM that demonstrates the problem. I think the problem you're having, however, is due to a bug in your NES program, not the emulators. It's just showing up differently on some emulators than others.
Sorry, just wanted to draw more attention to my issue, incase people don't view the other thread.
People on these forums with the knowledge look at every thread in every section all the time, basically.
Still, it blows my mind that you pick an un-understood (in some parts?) mapper over something better, like MMC3, which is much easier to work with.
Locking thread due to previously-mentioned dupe (effectively).