Emulator

Game Name?
Super Paper Mario

Game ID?
R8PP01

What's the problem? Describe what went wrong in few words.
In Super Paper Mario, the transitions are non-existant. Entering a door, going down a pipe, etc. This also makes the game uncomplettable, because transitions also don't release pixls (partners) that are required for completting the game. I made these videos to show my problem:
https://mega.co.nz/#!ZxhxXAwA!aAXHu2kWN0KZX-4EAuHzxnci2gVyGE1NvAe7lcmExsU

What did you expect to happen instead?
This game has small cutscenes when you do certain actions, such as going through a door. Doors being opened, after which the character goes inside, and it closes after him. Or when you go inside a building, there is a transition effect going across the screen. Or when you go through a pipe the character is being split into small squares.

What steps will reproduce the problem?
The easiest way to check if the emulator has this problem from a clean save file:

1. Sit through the prologue
2. Right before the first red door that leads to Chapter 1 notice what happens when you press up
3. If the doors opened, there is no problems, however, if the screen just faded to black without doors opening, there is a problem
   You'll notice more weird things happen as you play through the game, such as pixls disappearing and you're unable to use them

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?
All versions after 4.0-5915 including the latest 4.0-6068 all have this problem

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
Dolphin 4.0-5908 and before all work properly

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
OS: Windows 7 64 bit
CPU: AMD Athlon II 2 X2 240 (2.81 GHz)
RAM: 2GB
GPU: GeForce GT 240

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
Videos:
https://mega.co.nz/#!ZxhxXAwA!aAXHu2kWN0KZX-4EAuHzxnci2gVyGE1NvAe7lcmExsU