Here's mine, though I only do the initial ripping under Win7.
- Rip with AnyDVD HD
- Extract video / audio / subtitles with ClownBD
- Convert the subs with BSup2Sub
- Mux everything back in with mkvmerge
I then do then encode with HB on my iMac. For a much more detailed explanation, have a look here.
HTH....
Here is my work flow for Apple / Microsoft mixed environment:
- DVDfab Blu-Ray Ripper mkv.remux preset with subtitles to idx files (you can enable Intel Quicksync for faster remux)
- MKVmerge GUI to remux the subtitle tracks into the mkv created by DVDfab (different source and destination drives will increase speed)
- Handbrake Apple TV 2 preset (720p) or High Profile preset (1080p)
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I used your High Profile CQ RF18 suggestion - and it worked flawlessly - and played perfectly on AppleTV - however it will not play on my iPad 3 - are there specifications that are different for iPad 3 that would cause this to not play?
The bit rate is probably too high, you can try toggling between Strict and Loose as sometimes that helps playback compatibility. However, it's likely the content is causing too high a bit rate at RF18 for the iPad.