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Anybody have any recommendations on a good encoding program that is compatible with Win8? I was using Handbrake on my old Vista PC but it doesn't look like it supports Win8 for my new PC.

Handbrake should work fine with Win8, it's just that there's no Metro interface so you'll have to switch to desktop mode.

Handbrake works fine on my Win 8 box.

there are other options on the 'video file conversion - mts' thread going on now too.