Subler seems to work well to mux audio and video from an M4V with SRT caption files. These play nice with QuickTime player, iPads and iPods etc. Note adding SRT with Subler is for subtitles, not closed captions. Closed captions in .scc format can be muxed into the M4V with Compressor (in the Additional Information tab) on the original file in the compression queue. Neither of these methods seems to trigger a “CC” icon in iTunes or iTunes U apps.
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