Emulator

Game Name?
Metroid Prime

Game ID?
GM8E01

What's the problem? Describe what went wrong in few words.
As of 4.0-4583, there are various video issues when playing Metroid Prime using the Direct3D backend. The charge beam's shots have a large black box surrounding them, and the Phazon Suit's glow no longer renders. There are likely more issues that I didn't notice.

What did you expect to happen instead?
I expected the game to play as it has in previous builds.

What steps will reproduce the problem?

1. Load into the game.
2. Acquire the charge beam.
3. Fire a shot.
4. There will be a large black box around your fired shot.

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?
4.0-4583

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
Yes, 4.0-4577

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
CPU: Intel Core i7 3770K at 3.5GHz
GPU: Nvidia GTX 680 (Driver version: 344.75)
RAM: 16GB 1600MHz
OS: Windows 7 Ultimate x64

This bug has also been confirmed on my friend's computer.
CPU: AMD A10-7850K at 3.7GHz
GPU: 8-Core Kaveri GPU on the 7850K (Driver version: Catalyst 14.12)
RAM: 8GB 1600MHz
OS: Windows 7 Home Premium x64

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
Video of the issues: https://www.youtube.com/watch?v=O3lf9VsoZlk