hi david,
there are several issues with your file... and -- sorry to have to tell you that -- you're doing a bad job in describing your issues.
you're mostly trying to find errors in scribus, while there are good changes that the errors come from the way you setup your workflow.
as i already wrote, the first step will to fix your left and right master pages in the .sla, first. (if you want a double side layout you should put left master pages on the left side and right master pages to the right!)
alnse, since scribus semmes to correctly produce the pdf (you have not brought any evidence that it would not be that way), the error is produced by the way your pdf reader (hopefully acrobat) talks to the printer driver.
summary: scribus is doing what you tell him to do... and when you print from your pdf reader there is something happening, that you don't think should happen: so, fix your scribus document and check that all the settings in the pdf reader are correct!
ciao
a.l.e