[Skank]

There may be something up with your rips then possibly, as this doesn't happen with about a random dozen tested of my approx. 200 3D disc rips. I'd try a couple of things... if they're full disc rips, do movie only using tsMuxeR to rule out seamless branching as the culprit, and try MVC MKV container (as Zidoo X6, HiMedia H8, and Pi2 support it).

Don't think so

Cause it happens when i dont touch the iso, it happens when i do touch the iso and rip out movie only..

No matter what, it always has the problem.
I dont understand why you dont have it... i really dont perhaps you dont fully watch the movie in 2d ..

I'm gonna try remuxing again

But in fact, it should just play like any other mediaplayer does, dont want mvc mkv either, cause its not supported widely... only mvc iso