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?
Yes. I don't really understand using the 1:01 (I used 1:00 also), but in either case, I get no change after transcode.
I was also using an automatic transcode. It shouldn't matter - transcode for DVD has to go to DVD legal output.
I can't imagine what produces this result.