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But I can't get it to work. Permute is set to PAL, but perhaps the mkv's are NTSC, not sure.
Permute is set to DVD - I convert the MKV and out comes an ISO file.

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It sounds like you have created a data DVD with an .mkv file. There are DVD players that play data DVDs, but I am aware of none that play .mkv. The DivX format is popular for data DVDs. Media DVDs store content in the MPEG-2 format. Both Roxio Toast 11 Titanium and Toast 11 Pro support .mkv. My guess is that you are not taking the step to convert your .mkv prior to burning. Everything should be doable within Toast.
 
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