General journal entries negating each other in tax reports

I have been trying to use General Journal entries to cover off a couple of transactions, but something I am doing is causing there to be two entries in my Tax FastZoom reports, which cancel each other out. 

An example was a repayment of a shareholder loan:
Debit Liability
Credit Bank Account
Shows up in the NCF Tax FastZoom report on two lines, one negative, one positive, therefore not impacting the total.

Similarly sales (which I'm only using the General Journal due to the difficulties of Reckon BankData rules, which I think I am going to stop using after realising that I had to re-enter every eftpos sale for the quarter as each entry negated itself)
Debit Bank Account
Credit Sales
Having it appear twice (negative and positive) then totally skews my sales figure for the BAS.

I thought I understand the basics of double entry accounting enough for this to be right, but clearly not!

Where am I going wrong? What should the entries be in these instances? Do other people use BankData to enter daily EFT receipts, and get meaningful transactions from it?