Emulator

64 bit Dolphin, sorry missed that.

Use EFB to Ram for the map to appear properly. Also you'll need a higher texture cache accuracy.

http://wiki.dolphin-emu.org/index.php?title=The_Legend_of_Zelda:_Twilight_Princess_(GC)

Just tried no luck.

Try a version around 3.5-1200, and use EFB to Ram with safe texcache accuracy. I know it works there. How about for you?

Need to download an older version. Do it when I wake up. Thank you very
much. I'll follow up later with you.

It doesn't happen with an Nvidia card and Direct 3d11. Probably Intel IGP related?

With DX9 it does not happen. Also that igp will do 60 fps in most games.
Not bad.

I tested on Intel HD4000 and a GTX 280, and it only happens on the Intel HD4000. That is the source of the problem, likely because it doesn't fully support D3D10/11. Stick to a different graphics backend, or use a computer that has an actual graphics card.

Everything else in the game seems fine, so I doubt that someone could not
step through it in a debugger set a break point as the layer is draw then
overlaid onto the textures behind it. Seems like an alpha channel or FB
effect is not blended or clipped all together. This is something DX
supports on HD 4000. If you look the map is correct, the area around is
blended incorrect. Maybe a muti texture issue. I'm not sure just
speculation. Thanks. Remember Double Dash intro for the longest time, now
it's there.

That's true as well, I was just thinking on the grounds of it being an intel bug. I don't know how keen they'd be to put a work-around. I guess that's why I'm not working on the emulator. At least we know it's something to do with the Intel Graphics Accelerator. The best thing you can do is go through older builds and see if any of them worked, and then narrow down to the build that started this issue. If it's always happened, and it only happens on one back-end with a graphics card that isn't fully supported, the chances of it being fixed are definitely lessened.

Also most graphic cards even igp's share the same MFC api's to achieve the desired effects it's how each implements these effects that differs.

Here's an example. With Project64 2.1 using Jabos DX8 1.7-57, playing Mario 64 I lose shadow effect under Mario's feet and under the 2d billboard trees. Looks like Zbuffer issue. Now when I use Glide64 pluggin that came with the emu all is ok, and Mario has the desolve effect. So one could say there is a bug with the drivers and HD 4000 or you could say it's a function handle differently.

No, your driver just doesn't properly handle what the plugin does. The plugin isn't wrong, your graphics card is. Because Glide 64 is older, it uses older, likely slower or even less accurate methods (I think just older/slower, I love that plugin) where as the newer plugs probably use features that only semi-functional graphics cards.

Intel's integrated chipsets are notoriously bad at handling things.

Off to the races then.