Emulator

Game Name?
Legend of Zelda Twilight Princess

Game ID?
RZDP01

What's the problem? Describe what went wrong in few words.
During the boss battle with Diababa you are supposed to use your boomerang to hit the bosses head (and optionally after the first round, "arms") with bombs. When the bomb reaches them, it is supposed to impact the head or trigger an animation for the arms. However, while this usually works fine with the "arms" Diababa's head is almost never struck, instead he only makes the animation like you hit him with only the boomerang, and the bomb returns to you roughly 95% of the time. In, fact the only sure fire way to "hit" him is to aim behind him instead of targeting him and the bomb will pass through part of him and explode(still a low chance but better than the normal way. However, the boss gets hit with the bomb more often the first time you hit him, so you'll probably be able to do it the first time, but not any time after that. This issue also affects his "arms" to a much lesser extent, but you should still be able to hit them 9/10 times.
D3D and OpenGL backends.

What steps will reproduce the problem?
[Don't assume we have ever played the game and know any level names. Be as
specific as possible.]

1. Enter the forest temple boss room with any settings (game settings and hyrule field hack seem to make no difference.

2. Grab a bomb bug from the logs with boomerang and boomerang his arms, then the head will appear.

3. repeat with bombs boomeranged from the monkey and experience frustration.

Dolphin 3.5 and 3.5-367 are old versions of Dolphin that have
known issues and bugs, so don't report issues about them and test the
latest Dolphin version first.
Which versions of Dolphin did you test on?
4-2450 4.2 stable and my own build with a few extra d3d features

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
I do not know if an older version worked, but I would imagine so, seeing as this is a mandatory boss fight in a fairly popular game, then again last months mario party glitch.

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
windows 8.1
nvidia 660m
i7 3630qm

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
[Upload big files to a hosting service and post links here!]
here is how the boss fight should play:
https://www.youtube.com/watch?v=D0kGgsGIaRQ
savestate D3D backend default settings no cheats or field hack dual core+idle skip: http://www.mediafire.com/download/rlqa8274bha7at6/RZDP01.s02

p.s. anybody else get some flickering textures in this dungeon on D3D? I think its just me, but not sure.