In the meantime, it has turned out that the new beta of MP4Tools fixes the subtitle problem - and is way faster & more reliable. Make sure you use it and not the regular version. Download from http://www.emmgunn.com/betadownload.html
Do you have any problems with batch loaded files? I'm in the process of remuxing my movies (over 1100) from mkv to m4v (mp4), keeping the original surround sound track and adding a 2-channel track to make them stream ready for ipad/iphone (I use Plex at home, mkvs are fine, trying to eliminate transcoding for i-devices). The beta version does seem to cure any audio sync issues, but doesn't add a 2-channel audio track when more than 1 file is loaded.
Basic settings are video/audio pass through and add 2 channel audio track. I've exchanged emails with the developer, but nothing recent. Thanks in advance.
*Can Subler pass through multi channel audio and add a 2-channel track? Seems to me it wants to convert only, but I've only toyed with it.
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