ZSNES totally borks the map in EB. I haven't tried it in SNES9x or SNEeSe, but I hear they both have issues. No idea what those issues are.
Super Sleuth has a tiny glitch when the map is scrolling around at the start.
bsnes has displayed the map perfectly since v0.013. The only issue in bsnes that I'm aware of is that on some screens, the mosaic will wrap around the screen (from the left to the right or vice versa) and show up on the first 1-8 pixels or so. It goes away when the mosaic is turned off again. I don't know if the real game does that because the edges are cut off by the TV screen. If anyone will verify this is a bug, I'll go ahead and fix it. Of course, in return for using bsnes you'll need a PC with at least a $100 processor, and you'll have to give up savestates and stick to save RAM only.