Jan diagnosed the problem with Encore four years ago 😃
On x264bluray.com they say that Adobe Encore CS5 has issues with BD compatible streams if --open-gop is enabled, which it is in this case. I don’t know if this applies to all versions of the software or if they fixed it, but as we’re talking about Adobe here, the issue is probably still present.
It sounds likely that a more compatible stream could be encoded with different x264 settings, but aside from that the aforementioned bait ‘n’ switch method should do the trick.