Ah, my software’s pretty purpose-built. Project Threepio doesn’t have any overlapping or even immediately adjacent subtitles–so just going over the logic in my mind, I imagine the SUP will end up having two distinct subtitles with overlapping timings and the same onscreen placement, which will likely behave badly as you describe. If it was smarter, it would probably create three adjacent subtitles, one for each distinct subtitle, and another for both subtitles showing at the same time, with placement adjusted, etc*. It would not be an easy change to the existing script, it would be a whole back-to-the-drawing-board type change.

So while my scripts have all the fancy features I wanted, it’s actually not nearly as feature-rich as other software (or else it’s simply broken) with regard to things that don’t apply to Project Threepio.

* Also, in my brief flirtations with immediately adjacent subtitles, I’ve found that not all players even do that very well, at least right now (they flash, they don’t show up, it’s a crapshoot). If you’re trying to make compatible subtitles, always leave a gap. It could be half (or more) of the problems you’re seeing are with the player, not the subtitles. *cough* especially if you’re using VLC *cough*