Hmm, I'm not actually able to reproduce this. I've tried various render settings and media item take offsets, etc.
Could you possibly trim the project down to just the one track with one media item and send it to us at support at cockos?
[edit] I think you have track FX that's being rendered as well, because the stereo render doesn't look like the top 2 channels of the 4-channel media, right? Does the marker embedding problem change at all if you remove the track FX?
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