Isuues discovered with invoicing at BAS time

I just completed my first BAS, and it seems that MYOB cannot handle the way I Invoice.

I have an accountant who ran my BAS for me. However, when reviewing the sales and purchasing data, I thought, "What the hell is going on here?" It turns out that in three months, the system is reporting that I did over $42,000 in sales, when I have only invoiced for about $21,000.

The system adds every single line of the invoice and, in some cases, the Invoice total as well.

Is there a way to ensure that the MYOB System only adds the invoice amount to cash receipts, rather than every line of the invoice plus the invoice total? 

I am officially 6 months in to my MYOB experience and thought I was doing well, until I had to overpay my GST Owned amount.

I need to get this right, otherwise I might as well keep a written ledger.

Any thoughts or ideas appreciated.