Which version of the print agent are you using ?
We suffered from a similar issue which was resolved by changing the type of Print Agent used.
IFS Print Agent Dot Net installation version.
Are you able to attach examples of the output showing the differences ?
Are the POs created using Report Designer or Crystal Report layouts ?
Do you get the same output issues for more report and printer combinations ?
\\svps19\PR2146 → direct print (Windows Standard Printer)
IFS Print Agent PR2146 → same printer thru Print Agent
0106_001.pdf = Purchase Order (Report Designer Standard TREX-Reports)
0108_001.pdf = Order Confirmation (Report Designer Standard TREX-Reports)
Did you ever resolve this issue? We are having the same issue today.