I have a similar issue in that I can't create Blu-ray discs from Encore directly so I have to create an ISO. The disc plays fine with the exception of not playing audio tracks 2, 3 or 4, it only plays the audio from track 1, in stereo.
Like you, everything plays fine in both Encore and Premier. Argh!
I burn the ISO using Image Burn.
If there's anyone out there who knows what's wrong, Please help!
Thanks