Emulator

Stop using the FPS patch; PAL60 will work in the latest builds.

Please bisect to when the bug happened; 500 builds is too many for people who cannot reproduce the issue to deduce what's going on. Find the build that caused the regression, then it will be easier to debug.

Thanks for your response! Good thing to know that I can use PAL60 for Xenoblade Chronicles, too! :)

Unfortunately, this issue is not related to Xenoblade Chronicles, I've tested various other games with 3DVision and got the same problem. Although I didn't get any crashes today, the games started to stutter and the eyes kept swapping like the 3D glasses did have a different frequency. Even build 4.0-6712 has the same issue, so this seems to be related to one of NVIDIAs 3D Vision Driver Updates and not to Dolphin. Seems like they've changed something in their API or whatever.
I am on Driver 353.30 currently.

Here's a video of the bug on Mario Kart Wii: https://www.youtube.com/watch?v=ZSeY3AFmINs

I will try it with an older version of the driver. If that doesn't help, I will just reset everything on my system when I upgrade to Windows 10 to see if this helps...

Okay, using 4.0-7103, the issue seems to be reduced to some lag, like 50% of the original framerate. No wrong frequency of the 3D glasses anymore, no more sutter. Gonna investigate further...

I tried using 353.30 (newest NVIDIA driver) and 353.06 (the driver everything used to work under a month ago). No differences. However, the 50% framerate issue that I only got under 4.0-7103 and not under the older versions that I tested, is not limited to 3D Vision, but appears under all 3D modes (like side-by-side). Guess this problem changed a bit over time...
It is very interesting that using the builds that gave me crashes and the left-right-swap on the glasses, the framerate seems to be no problem (besides the lag spikes I get once in a second)

That's really weird. Can you go back to even older builds? Find a build that doesn't do this? Then work forward until you find the cause?

Do you experience the same issue with the Side-by-Side mode or just the Nvidia 3D Vision mode?

Like I said, I experience it with all modes. But somehow I also get slowdowns and lags and increasing input latency over the time. Seems like my Dolphin installation is completely broken. I will upgrade to Windows 10 tomorrow, after this upgrate, I will reset everything on my PC, let's see if it works then :/

Well, now I am on Windows 10. What can I say? It works perfectly (4.0-7147). No latency, no 3D issues, no slowdowns, nothing :) I could even record using ShadowPlay while playing in 3D and got constant 60 FPS :) I really love this emulator. And obviously I hate my PC for being so mean to me... I even did reset my whole Dolphin config, so this issue must have been caused by something else.

Looking forward to 5.0 and new features. Maybe Direct3D 12 at some point in the future?

And sorry for causing so much trouble with this report :(