my apologies if I was confusing, I am using anydvd to rip the original DVD to an ISO, from there I am using handbrake to encode the ISO to a MP4. originally the issue was anydvd was not ripping the DVD correctly because I was using an old version of anydvd, then I downloaded the current version of redfox and was able to get an ISO that plays correctly, which brought me to the question I originally of
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so I downloaded 8.0.9.0 and was able to rip hacksaw to an ISO, then proceeded to use the latest version of handbrake, but the resulting MP4 has the out of order chapters issue, I assume this is due to handbrake not encoding the ISO correctly, I read on here about setting the chapter order, but have yet to find were in handbrake this is done, or is it done in anydvd somewhere?
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so that is why I was thinking it was a handbrake issue.