This is complicated, so bare with me... 
Squirrelcart does not have the means to send accurate dimensions for a shipment to any RTR courier, unless you check "Ship as a separate package" on your product records. If every item in your store had that field checked and your dimensions and weights were entered correctly your real time rates would be 100% accurate.
However, for items that may ship together with other items in the same box we have no way of determining what the size of that box is going to be because we don't know how you will be packing the items. Because of this, when "Ship as a separate package" is not checked we normally do not send dimensions along with rate requests.
UPS, FedEx, and USPS allow you to make rate requests without sending dimensions. AusPost does not. If you try, it reports that the dimensions are missing.
To account for this, if a rate request for AusPost is made without dimensions we default the dimensions to their smallest measurements allowed. That number is 5 cm. Due to the way we handle dimensions (which is too complicated to explain here), we've set the default measurements to 2 inches which is equivalent to 5.08 cm. AusPost requires dimensions be sent to them in mm. So, we then convert the 2 inches to 51 millimeters which is why you are seeing 51x51x51 for those orders.
We will be completely revamping our shipping features in the future, and are looking into adding a feature that would allow you to specify how certain items ship together and in what size boxes. Until that time, we have no way of sending accurate dimensions for orders like this.
To get very accurate rates, you can mark all your products as "Ship as a Separate Package".
The other alternative would be a workaround. If you want to make the rates more accurate you can change the default measurements used from 2 inches to something more practical for you. You can do this by editing the file squirrelcart/functions/storefront/shipping/australia_post.func.php, changing lines #49, 50, and 51 to your new default measurements in inches:
PHP Code:
if (!($width > 2)) $width = 2;
if (!($height > 2)) $height = 2;
if (!($depth > 2)) $depth = 2;
So, if most of your shipments are at least 12 in. x 9 in. x 6 in. you would change that code to:
PHP Code:
if (!($width > 2)) $width = 12;
if (!($height > 2)) $height = 9;
if (!($depth > 2)) $depth = 6;