Emulator

Game Name?
Probably all
Tried with:
Metroid Prime
Metroid Prime 2
Mario Kart Double Dash
Luigi's Mansion
Mario Party 7
Super Smash Bros. Brawl

Game ID?
GM8P01 (Metroid Prime)
G2ME01 (Metroid Prime 2)
GM4P01 (Mario Kart DOuble Dash)
GLME01 (Luigi's Mansion)
GP7P01 (Mario Party 7)
RSBP01 (Super Smash Bros. Brawl)

What's the problem? Describe what went wrong in few words.
The first time I boot a game it renders perfectly on 3D. If I stop the emulator (and even restart my computer!) the next time I try to run that game with 3D enabled it will simply fail to render it. Sometimes leaving just a black screen with all the sound and game still playing (I can hear the intro, menú options, character selection and even the race going on on MKDD), and sometimes it will fail to render some objects or show odd polygons.
If I try to play other game, it will fork, for the first time, then will fail.
Another game, work; relaunch, fail.
Each game can be launched successfully only once
If I try to run a "3D broken" game normally (Without 3D) it will play perfectly, enabling 3D again will make it fail
Enabling 3D on-the-go will make it fail to render. Disabling 3D on-the-go will show the game normally again.

What did you expect to happen instead?
The game to always start playing like the first time

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.Set Graphics to OpenGL and activate 3D; any 3d will work
2.Start a game and it will work
3.Stop the emulation and try to launch it again

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?
Dolphin 4.0-6446

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

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
I've always used D3D for playing games, even in stereoscopic 3D. But a PR (https://github.com/dolphin-emu/dolphin/pull/2491) added a shadder for OpenGL to use anaglyphic with different colors (Magenta-Green and Amber-Blue), so I decided to try them.
Also, some pics:

Metroid Prime 2 (All with Magenta-Green anaglyph 3D)
Just after loading a game, when the game shows Samus and a save station
http://s10.postimg.org/7xaowjsjd/G2_ME01_1.png
Once game starts and you can play; shoot, jump, etc
http://s10.postimg.org/tm9l0eurd/G2_ME01_2.png
Morph Ball!
http://s10.postimg.org/4svfm0md5/G2_ME01_3.png

Super Smash Bros Brawl:
Main menú side-by-side
http://s10.postimg.org/61nwle3p5/RSBP01_1.png
Main menu with normal Red-Cyan anaglyph 3D
http://s10.postimg.org/4p67ji69l/RSBP01_2.png

I also noticed that as I try to launch a game some more times it would break worse
At first I launched MP2 fine, the second time I tried it failed to show me the Nintendo logo, but it rendered the Retro Studios logo and the Title screen and the menú kinda worked. It was shown but the text labels of the menú were invisible. Then I tried to start the game and it showed me those weird polygons.
After some more tries (like 5-10) it was just black screen until it showed me those polygons.