You mean a multi-purpose bay - now I'm with you!
BTW thanks for locating the manual online - it is an excellent way for others to help you.
Have you tried swapping the primary battery with the new second battery in these slots (i.e. putting a fully charged secondary (new) battery in the primary battery slot, and then putting the original battery in the multi-purpose slot) and starting the computer from cold? Try also starting the computer from your fully charged new second battery firstly in the primary battery bay, and then in the secondary bay. Do this for the primary battery. If both work OK it suggests that the multi-purpose slot works (at least for the batteries).
Failing this contact Sony for support. You will find the number on VAIO-Link. under Contacts. You can try eSupport as well, but it may take time for a response.
