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Yes, the 3 original discs are BD50. I was simply creating a backup of each onto 3 separate 25GB discs. The SD video files inside the m2ts containers are mpeg-2.
When starting the x264 encoder, the first line shows "lav [info]: 720x480i 32:27 @ 30000/1001 fps (cfr)". If you import the same file into Handbrake, the dimensions tab shows: "Source 720x480, PAR 32/27".
Those references to 32:27 made me suspect the black bars on the BDRB copy were caused by the SAR 40:33 in BDRB's x264 command line. I found that if I used SAR 32:27, or if I just omitted the SAR parameter completely, both scenarios produced video identical to the source, with no black bars.
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