I just had to do four years' worth of this for tax purposes.
The way I worked mine out is by grabbing my trading summaries (not the net buy/sell, the actual transactions). Only focus on the SALES, because you don't claim the loss or gain until you sell. Whatever you've sold, subtract the purchase price from it. I use excel to chart all this, which makes it fairly easy. It often includes keeping a list of prior FY trades open for shares bought in a previous FY.
If you sold something for $1400 (net of brokerage), go back to the buy and subtract (net of brokerage). So if you sold for $1400 and bought for $1000, it leaves you a profit of $400. Using figures net of brokerage means you don't then need to subtract brokerage separately. Trade execution values are normally net of brokerage, so that's easy anyway.
The total buys and sells from the Commsec statement in every FY bore no resemblance to my actual P&L. IMO, just ignore these and focus on the sells that were executed and their corresponding buys.
If you have another job and trading isn't your primary source of income, my understand is this would make you to be a speculative trader which would make income and losses part of your normal assessable income, not capital gains/deductions. If you have an overall loss, this means it may come off your taxable income. If it is a capital loss, my understanding is it can only be deducted from capital gains.
Not advice as I am not a professional and know nothing of your personal circumstances. I do suggest speaking with another accountant if yours can't explain why they have included figures the way they have.
You're right to seek additional info, maybe just not on this forum. Never mess with the tax man
