Some more checking using wireshark on the destination server.
I created a simple html page that is contained under a directory that requires SSL and a client certificate, as configured in the apache configuration.
This works fine from the IE and Firefox desktop browsers.
Now, using Safari on the iPad with the appropriate certificates installed (client cert and CA cert) using the profile management tool, I attempted to connect to this page.
Wireshark shows the iPad contacting the server and the TLSv1 protocol selection (Client Hello and Server Hello).
Following this the server issues the requested server certificate and the CA cert to the iPad device.
The iPad device responds with an ACK and this is where it stops the communication. No further packets appear.
During this time, the iPad has requested that a client certificate be selected using the dialog and the appropriate client cert is selected, however the network transaction does not show the iPad ever sending this certificate to the server.