Take the QuickTime files from MC, bring them into AME. Transcode there.
Then bring those transcoded assets into a new Encore project.
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I am having trouble tracking your multiple workflows, in part since I don't know what program you are using to play files when you say they played back successfully (Encore preview; other program etc). Don't worry about explaining what you wrote above, just provide a bit more info when you report your next tests, starting with Jim's suggestion.
Other forum posting have talked about a 2-pass VBR error and some other things, but that doesn't seem to be the problem as I did a test using that same couple minute excerpt quicktime with different settings, and all played back (2-pass vbr 4.1 level, 2-pass vbr 4.0 level, 1-pass vbr 4.1 level, 1-pass vbr 4.0 level, etc).
I think the 2 pass vbr bug is not always apparent when you transcode short clips.
To followup, I build the blu-ray as an image, then burn the image to a 25GB BD-R, and playback on a Panasonic DMP-BD60.
I just encoded all the videos directly within AME using the default preset "use source attributes, highest quality" and they imported in Encore perfectly. I'm leaving the project to build, and I'll report in tomorrow morning. One thing I noticed is that while building it said "transcoding" for each of the videos, though it was done with that step pretty fast (maybe 10 minutes for all 3). I'm assuming it wasn't transcoding the video, but maybe the audio (.wav).
Yep. All the presets use WAV audio.
Tested the blu-ray out in our player this morning. Seems to play fine. Thanks for the tip.
Looks like the one SD video somehow had it's interlacing reversed so I'll just have to manually set that and re-transcode. Should be good to go otherwise.