If the padstack for the TH header does not have 'plated' checked you might get this; othewise it is very odd.
This sequence is how I would do it:
Select the bottom layer (<F4> to toggle between routing layers - the bottom layer must be a routing layer for this to work)
Select your TH header
<F2> to start routing
Route to your SMD
Thanks for the response; it turns out the via bias settings were
preventing me from routing on the top layer. Now sorted thanks,