Popcorns expand when they pop, because of the moist inner of the pop corn, depending on the corn, the number of unpopped kernels varies.
P225 exhibited the highest (47%) number of unpopped kernels, whereas
AP416 (27%) was higher than P615, P612, P415, and EXP92233 (around
16%). AP414 was the best hybrid as it had the least number (4%),
whereas the remaining hybrids had 9-12% unpopped kernels.
Taken from the paper "Role of the Pericarp Cellulose Matrix as a Moisture Barrier in Microwaveable Popcorn" by "Agung S. Tandjung".
Number is usually around 10-20% was how I took it from that paper.
http://pubs.acs.org/doi/abs/10.1021/bm049220l
There is not any crazy reasons why the numbers doesn't match. On popcorn packages they estimate how much popped popcorns the end result will turn into. I thus assume they take in consideration that not all kernels pop.
In the estimation on the amount of popped popcorns you will get they the number thus is lower than if all kernels popped, and if you multiply estimation with their energy value you will fall short of the unpopped's energy value.
This is simply math, not some magical phenomena or butter being stuck inside the bag. 15% of kernels doesn't pop in their estimation, most probably, which is why if you multiply estimation with popped energy value only get to 85% of the energy value of the unpopped kernels.

Popped Vs. Unpopped: Calorie Comparison
Many people wonder why unpopped popcorn has more calories in
comparison to popped ones. The answer lies in popcorn kernels, popped
popcorn has less kernels, therefore less calories. What I mean to say
is, a cup of unpopped popcorn will have more calories because of the
large number of kernels that are present. On the other hand, popped
popcorn of the same measure will have less calories because of the
absence of kernels. Moreover, a cup of unpopped popcorn will give you
around four cups of popped popcorn. Therefore, the former has more
calories.
The popped popcorns have less kernels. Why? Because not all kernels pops.
http://www.buzzle.com/articles/popcorn-calories-popped-vs-unpopped.html
I asked "Garret Popcorn Shop" if my assumption was correct.
From: C193181 Daniel Hambraeus Sent: Wednesday, February 20, 2013
07:26 am CST (GMT-06:00) Subject: Nutrition
Hello. On popcorn packages it's listed that X amount of unpopped
popcorns turns into Y amount of popped popcorns. In the energy
listings there is values for popped popcorns and unpopped popcorns. If
you multiply the popped popcorn value with the estimated amount of
popped popcorns you'll get, the energy value is lower than for the
unpopped ones. Does this mean in the estimation that you take in
consideration not all pop corn kernels pop?
This is my original mail.
Dear Mr. Hambraeus, Thank you for contacting Garrett Popcorn Shops. We
appreciate your inquiry. You are correct, we do take into
consideration the ratio of unpoped popcorn kernels and it is for this
reason the energry value is lower. Please let us know if you have any
further questions or concerns!
Best Wishes,
Lauren Wilk, Garrett Popcorn Shops
This is the answer I got from Garrett Popcorn Shops. They gave an answer directly. The reason the values doesn't add up is because they take in consideration the ratio of unpoped popcorn kernels.