I have booked some flights with VH and managed to reserve seats with VS within 20 minutes of confirming the booking.

VH will give you a reference, as indicated in your post, like 123456/S09. This means nothing on the VS website. What you need to do is either ask VH or call Flying Club and get the PNR for the flight portion of the VH booking. That will be a six digit reference containing numbers and letters. This is the booking reference that the VS website need.

If you are calling Flying Club to gain the PNR you could always ask them to allocate seats for you. You'll then be able to go on the website and see the seats on the Manage Your Booking Section.

Hope it works.

Iain