it wouldn't have to move to get onto an appropriate GOP frame which to me is what it looks like Encore is doing to me when my marker is at say 1:01.
Encore (or Premiere for that matter) starts a new gop at a marker. So it should not matter, as long as you are dealing with non-gop material to begin with. That is what is very odd about this: export from Premiere, markers stay in place. Transcode in Encore, they do not. Either one, should do what Premiere is. For me, both work as they should.