First, note that the federal circuit has ruled on these patents before, and upheld them. http://patentlyo.com/media/2014/09/Virnetx-v-Cisco.pdf
Apple conveniently leaves this part out.
(i think it's a BS ruling, but it is a final appeals court ruling on the validity of the patents).
As for the PTO finding them invalid:
If you look at the file wrappers of these patents, you will see what apple means is "someone has requested review of these patents by the PTO, and they have initially been found invalid".
(Apple's request to review validity was in fact, denied)
Go to http://portal.uspto.gov/pair/PublicPair Enter the patent numbers Click "image file wrapper".
So they haven't "been found invalid", instead, they are going to trial before the PTAB to see whether they are invalid.
Note: On a number of these patents, Apple's review requests have been denied a number of times before someone else's review request was granted