Trade with your own money? Why would you ever do that unless you had to? In my experience comsec would allow you to place an order up to the value of your current cleared available holdings. This gives you the option of doing a bit of contra and selling up an equivalent holding on T2 - on T3 the difference is credited / debited to you account. I do quite a lot of trades like this (some call it scalping, I call it short term trading).
I have only ever had that message if I haven't settled on T3 then they put you in the bad book for a while until you can show that you can manage to pay your bills on time.
Hope this isn't a new policy of requiring cleared funds, but from the message it doesn't sound like it. Ring them up and complain, if you do a bit of volume with them then they won't risk pissing you off and will take care of the problem.