I eliminated my source footage a variable by using generated title clips in my Pr sequence. Similar result in En as per my supplementary last response.
So you're saying you do a dynamic link from a sequence in Pr to En with a chapter marker at 1:01 and after a transcode the marker stays at 1:01?
... and you're using CS6?
My transcode was set to automatic, but I tried a couple of the presets like DV HQ 7Mb VBR 2-pass. I made sure the framerate was 29.97.
What setting could I possibly have to produce the result I'm getting?