Robert,
When using the OOTB print widget, or the PCHPrintSOE, the selection graphic is not showing up on the print at all for me. At 3.0 it showed but covered up the underlying annotation. In 3.6, besides it not showing, any annotation I have displayed shows up duplicated in the print.
Somewhat related...any graphics (draw or measure widgets) shown on the map do not show up on the printSOE. They do show on the OOTB widget however.
Is this something on my end or is this the case for everyone?