Emulator

Game Name?
Metroid Prime Trilogy NTSC,
Xenoblade Chronicles NTSC

Game ID?
R3ME01
SX4E01

MD5 Hash?
MPT: e7a1593ebdce96a2165d6b5bf5be0d4b
XC: 4e4115501935bceac0e77e573bbab152

What's the problem? Describe what went wrong.
The second eye in stereoscopic 3D has rendering issues when using exclusive ubershaders - either a picture in picture effect or a double image - see screenshots examples.
Hybrid mode works fine and disabled works fine.

What steps will reproduce the problem?
Enable exclusive ubershaders and stereoscopic 3d in DX11 or OGL mode.

It is important to make sure the bug hasn't already been fixed. Please tell us what the latest version you've verified the bug on.
5.0-5209

Is the issue present in the latest stable version?
No, ubershaders aren't in the latest stable version

If the issue isn't present in the latest stable version, which is the first broken version?
N/A

What are your PC specifications? (CPU, GPU, Operating System, more)
i7-4770k @ 4.3GHz
EVGA GTX 1080Ti
16GB 2400MHz DDR3
Windows 10 x64

**Is there anything else that can help developers narrow down the issue?
Screenshots included