The branched Blade Runner disc is identical in the newer set (as is the Final Cut) - it's just the workprint that received the AVC re-encode since it was being compiled together with the SD special features on one disc.

I checked anyway and those settings are identical. What other branched discs are there to look at? I'll have a look through my collection.

Perhaps I asked the wrong question about the m2ts files. The excess 11 seconds might not be black, but rather redundant footage, e.g. does clip B begin with the last 11 seconds of clip A?