After I posted the "More Info" post, Jamie mentioned something from her time as a captioning activist some time ago;
"Long ago I was told that when the media format changes, e.g. from movie to DVD to television to internet, the closed captions are lost because of the altering of time codes on the media. Closed captions have to match up with time codes.
"In addition, I remember that in the early days there was discussion about how because captioning is a service, there may be issues with payment. That is, if Company A pays for captioning then gives the media in a new format to Company B with captions included, then Company B saves money that Company A had to pay.
"But the bottom line problem is the loss of captions as media formats change. We need new technical solutions or more use of existing solutions. One way to save the captions would be to use the available tools CCExtractor or CaptionKeeper to extract the captions into a separate file before converting the media to another format. Then the captions can be refitted to the new media format (and this is a manual process as explained by Hulu).
"The deaf community and its hearing friends are going to have to pressure the original content providers to save captions before converting the media."
In short, by "issues with payment" in the second paragraph, the business that received the captioning services may not want to just give the captioned file/media to Company B.
Also, some utilities I've seen will remove the subtitles AND captioning when the movie is transferred from DVD to a format like AVI and/or send them to a separate file. One I've seen will do just this in PAL/NTSC conversions. I'm checking on the Matroska (.MKV) (Wikipedia entry) container, as it can hold many tracks in one file.