Warehouse Management - Ship GL Lines

We are about to start using warehouse management, I’ve set up a new location which contains bins with the require warehouse shipment option ticked. I now have an issue that when a warehouse shipment is created and posted, all item lines on the underlying sales order are correctly shipped but GL Account lines for miscellaneous charges are not. Is this a warehouse management set up issue?

The problem, is that when you post a Warehouse document, you only post Warehouse related entries. When you post your Warehouse Ship you only ship lines related to that document i.e. Items. If you do a Ship and Invoice on the Warehouse Ship, I belive it invoices the G/L Entries also.