tax help !!

I'm wondering if someone can help

My wife has been working out our profit and losses on shares sold for last financial year using software called Portfolio manager.

It seems that my Capital gains seem a bit high and that the software may not be taking into account the average price of a particular company

For example:

I bought TSE at $9, 7, 5, 4 and $1.25 over the last few years. I then sold some at $4. - however it is coming up as a capital gain on the software and yet my average price is $4 -(when you take into account the purchases at $9, 7, 5,4 and 1.25)

My question is: if i bought at 1.25 and then sold at $4 normally that would be a substantial capital gain - however, due to some purchases over the $4 mark would that not mean that a capital gain has not really happened.

Do we take into account the average price when working out capital gains?

If it is the case that you do take into account the average purchase price of a company then why is portfolio manager not taking this into account?

Some help would be appreciated as my wife has gone mad and is refusing to cook dinner tonight (LOL) unless this is resolved as we may have to pay back the family allowance due to my gross income increasing more than we thought due to the higher capital gains that is showing up in the software.

any help would be appreciated