How are you creating the invoice PDF? Save as | PDF or are you using print with the PDF option?
When you print, are you printing from a script or manually by selecting print from the file menu?
If you are using a script to print the invoice, does the script step show Print or Print [Restore]?
I'm guessing here that maybe the PDF is being generated from Print with the PDF option and then a script with Print is keeping that setting and generating a PDF instead of printing to the printer, but I could easily be wrong here.
If you are using a script, it might be informative to temporarily clear the "Perform without dialog" option on the script step so that you can see what printer options are selected just before you continue the script so that it prints.