FIXED IT!
After 2 days of searching for similar problems I found it & fixed it.
Encore CS3 wants to work with “Elementary Streams”. It will tolerate Quicktime files, but it doesn’t reference them well when it goes to burn a Blu Ray disc. Basically it seems that Encore has an issue remembering the location and names of files that it has transcoded – even when it has just transcoded them as part of the burn process.
Really Frustrating – as it would work some of the time with some files and not work most of the time.
So – the Fix. It took a while to figure out WTF an “Elementary Stream” was (either an h.264, or M2v for video, and or ac3/aiff(PCM) for audio). In order to get an elementary stream in to Encore I set up a custom compression using compressor (3.0.2). Compressor will let you create an Mpeg-2 encoding template for Blu-Ray( Imagine that). I set up a VBR 2 pass encode with 39Mbit as the high, and 33 Mbit as the low.
Took 10 minutes to process that and an ac3 file from my original (muxed) Quicktime file ( uncompressed 10 Bit 1920×1080 @ 23.976psf). Compressor will auto-detect frame rates, but I found that too spooky, and opted to create settings for 23.98 fps, and interlaced footage.
Upon re-creation and re-import of my assets into Encore I successfully built an auto-play 1080HD 24P Blu-Ray disc! Ac3 audio seems to give less problems than aiff audio so far.
..so much for beta testing this $1500 piece of not ready for prime-time Macro-Dobe SH**%.
Maybe it will work someday with out all of the rocket science in footage preparation. Till then I’ll stock with DVDSP for DVD’s, and hope that not so many clients want Blu-Ray.
FYI – My setup: 8 core Intel Mac(1st Gen), 5 GB Ram, 10.5.2, CS3 Master Suite + FCP Studio 2. Most footage from HDCAM- ProresHQ + Uncompressed.