When I play the m2ts file, it works fine in VLC and also in PowerDVD. That's interesting, but I'm not sure what that means?
If the actual m2ts file from the Encore build does not show the problem, but what I assume is the same file on disk (or in iso) shows the problem, what could cause such a problem? (I don't know.) The more frequent oddity is a problem on burned disk and not on iso or folder, which points to the burner, burn speed, or media. But that does not appear to be the issue here.
I can't find the example at the moment, but try creating a tiny bluray project and see if the problem occurs. If so, you can upload it for me to take a look.
For example, one menu with one button, linked to a 30 second timeline, using a sample of your material that is causing the problem. If that shows the problem, I would also try a bars and tones sample to eliminat your actual video - although I assume your video is part of the equation.