I have/had this same problem.
- I used the 2016 AutoCAD high quality PDF PC3
- I saved the drawing
- Started a new drawing
- Imported a layout tab and the page setup from the original drawing
- PUBLISH from the blank drawing
- all sheets are offset down and to the left by about the width of the margin (0.11")
I ended up putting an offset of 0.05, 0.05 mm into the page setup to solve the problem
In this case the plotted sheet size was 11x17 and the layout was scaled at 1:2 (1:2000) and the layout included a border that was exactly 11x17" that was not intended to be printed plus other items that were outside the margins. So I had setup all layouts by moving the edge of the border to the edge of the layout. As with the OP, it looks perfect in the layout and prints perfectly one sheet at a time but was offset by the publish command.
I believe the PUBLISH command includes some type of auto-centering logic because all my layouts were originally quite a bit off center and PUBLISH fixed that except for the extra undesirable offset. I think PUBLISH needs a switch to turn this feature off.