There's an errata posted on BoardGameGeek that corrects the rules about delivering Guild Orders, and an updated set of rules (from the publisher's site, also available on BGG) which includes the correction. According to the errata and the new rules with the errata included, you do indeed count the second order as a new order, and thus get more VPs than the first gave you.
• On page 8 under Guild Hall replace the last
paragraph with the one below:
IMPORTANT! – If you have just delivered a Guild
Order, then picked a new Guild Order and happen
to have the Resources with you to fill it, you may
turn them in immediately. Adjust prices and Orders,
and collect VP’s, as described above.
This is also confirmed by the designer in a thread on BoardGameGeek:
Brian has it correct, the guild orders are placed in front of you to track how many you have completed. The value of the delivery increases for each you deliver. Hence, 3 for the first card delivered, 4 for the second, 5 for the third and 6 thereafter. Let's say you deliver two at the same time, and they happen to be your 2nd and 3rd cards delivered, you would thus receive 9 on that delivery of two cards.
I do not have the original rules before the correction, so I don't know what it said; in particular, in the updated version, I see nothing about "you do not get to deliver the order," so I'm assuming that's something that the updated paragraph has replaced.