Got pointed at the right direction by alan storm,
answer was to call ->setDob('1999-1-15')
on the formData member of the block.
This is all within a class that extends Mage_Customer_AccountController
and the outline of the code is:
$year='1999';
$month='1';
$day='15';
$layout=$this->getLayout();
/*
The register block is a type="customer/form_register" template="customer/form/register.phtml"
i.e. Mage_Customer_Block_Form_Register
*/
$registerBlock=$layout->getBlock('customer_form_register');
$register_form_data=$registerBlock->getFormData();
$register_form_data->setDob($year.'-'.$month.'-'.$day);