Hi Jess,
I just tested my account and I am not experiencing that problem. All my line items are appearing using the SimpleInvoice template. Did you happen to alter it in any way?
In the Detail heading you want to be sure there's the following DetailReport: Invoice..InvoiceLine.Invoice. The DetailReport is where you'll enter the fields such as the Service Date, Items, Rate and Quantity. This will pull all the line items associated with a particular invoice.
Let me know if this makes sense to you.