We just implemented a script that emails invoices out to customers on a nightly basis. We use an Adv PDF template both for the manually printed invoices and the invoices emailed to the customer with the script. When we manually print the invoices, using the same adv template we are calling in the script, we get the shipping line in the list of items:

ITEM QTY BACK ORDER PRICE AMOUNT
103-0102-00       15                    $3.47 $52.05
MIC MUFF & O-RING KIT
103-0102-00        36                   $3.47 $124.92
MIC MUFF & O-RING KIT
UPS Ground                                 $15.00 $15.00
Shipment Method: UPS Ground

but when the invoice script (using a map reduce function) runs it produces a (render.create) PDF without the shipping line.

ITEM QTY BACK ORDER PRICE AMOUNT
103-0102-00       15                    $3.47 $52.05
MIC MUFF & O-RING KIT
103-0102-00        36                   $3.47 $124.92
MIC MUFF & O-RING KIT

We can see the shipping line item as expected in a saved search as well. Thoughts on what to look at? Known issue when rendering an invoice from a script?