No responses but I appear to have made some headway, which I'll share here in case someone's out there somewhere scratching their own head over this.
The problem seems to have to do with dvdauthor's STC discontinuity at the chapter points when it's fed one file per chapter; the initial pts/dts values are reset, and this somehow throws things off during playback, even if audio and video endpoints are perfectly aligned.
If the whole titleset is mplexed as one mpg and then dvdauthored with chapter- point offsets, the gaps disappear. Also, if the chapter points aren't aligned to GOP boundaries, dvdauthor will do it anyway and shift them backwards.
Bahman
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