Hi there, @SundayWST.
Thanks for posting your concern here in the Community. I'm here to help make sure that the custom data you enter will auto-populate when printing Pick List in QuickBooks Desktop (QBDT).
I check if there's an ongoing issue about this, but there isn't currently one. In this case, let's perform some troubleshooting that can help isolate this issue.
To start off, try closing all window inside QBDT by going to the then Windows menu at the top, then select Close All. Once done, reopen and reprint the Pick List again. Here's how:
1. On the Customers menu at the top, then pick Create Sales Order.
2, Click the TEMPLATE drop-down, then choose Intuit S.O Pick List.
3. Enter the necessary information, then select the Item(s) where you created the custom fields.
4. Click the Print icon at the top, then Preview to double check.
5. Once done, select the Print option to print the Pick List.
I also added some sample screenshots for your guide.




Just in case you need it, you may visit this article for more information: Pick tab in Sales Order Fulfillment.
That's it! Give this a try and let me know how it goes by leaving a comment below. I'm always here if you need further assistance. Take care and have a good one.