I noticed this problem last month and it has happened again today.
Booking.com seems to have changed a little in that a person can book two rooms against the same reservation code. When you click on the link in their email to you and you enter their extranet you get both rooms shown side by side (I only had two rooms booked so I don't know what happens if you have more) before I am sure you got two separate emails. It appears that Bed24 synchronises with the first room and not the second. I tried a manual sync on the second room and it still did not pick it up. So if you 'loose' the Booking.com email or it never arrives you will only reserve the one (and primary) room.
I think this is urgent and needs to be fixed quickly.
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