I have been comparing "good" MPEG-2s that load fine in Encore with the problem one, using MediaInfo.
The main difference I have found: in the "bad" file, although it has a VBR flag in its header information, MediaInfo does not load a "nominal bit rate" for it. "Good" VBR MPEG-2s load in MediaInfo with two bitrate numbers, a regular one and another one in parentheses. Apparently the parenthetical figure is the "nominal bit rate" per MediaInfo's tree view.
Bitrate Viewer shows a very flat bitrate line for the bad file. It has a few tiny spikes (not high) but overall, the bitrate is basically the same number throughout the entire file. On my "regular" MPEG-2 VBR files, the normal bitrate view looks like a mountain range by contrast.
I don't know why this would throw Encore off, but it's my only lead. Either this file should be CBR and its header information was written incorrectly by the camcorder, or it is missing a parameter (the "nominal bit rate" number) that a correct VBR file should have.
Not that I know how to change either one of these things!
