Thanks @Naedish . I did some digging in Sharesight and found the CGT options. I can see now why my sums and Sharesights are different. My SMSF is in pension phase, meaning we pay no CGT or Income tax. So, averaging my holdings seems the most practical. This makes the Sharesight reporting of little use, as its reports are very different to mine and the brokers. I would like to see a CGT/Income Tax option of 100% discount.
Talking with my brokers(CMC), they said their automated SELL does not sell from any specific parcels, (FIFO,LIFO etc) but average the entire holding…just as I do. Due to no tax implications, I have never asked the brokers to sell from parcels, as I would have to sell from the desk at greater cost per trade.
I can see now why my spreadsheet is pretty close to the brokers profit/loss sheet as we both average. But Sharesight follows the ATO CGT route.