Hi tibby
As a general rule the tax office says; It is the individual partners who make a capital gain or capital loss from a CGT event, not the partnership itself. For CGT purposes, each partner owns a proportionate share of each CGT asset.
http://www.ato.gov.au/nonprofit/content.asp?doc=/content/43486.htm&page=6
You have a tricky mix with CGT and partnerships. I guess it depends what you mean by 'joint', whether it is strictly a partnership or a shared account. In other words are all shares bought in joint names or do two or more people use the same account but buy in individual names. In the former I reckon you would have to split, in the later you would proportion.
What I would do is talk to your accountant first because with CGT there are different treatments, depending on how long ago they were purchased as well as whatever your particular 'joint' arrangements are in terms of the tax law.
I'm afraid it is not a simple answer. But, particularly if it involves a lot of money, I would get professional advice first to see if there is anything you can change to improve your particular set-up.