The issue ended up being a problem in the LabKey server when there were multiple R scripts referencing each other (i.e. in that case the outer script's prolog was the one being displayed in the PDF report). There was an issue opened for release 16.3 for this issue and has since been resolved with r48647:
https://www.labkey.org/home/Developer/issues/issues-details.view?issueId=28946
-Cory