It's strange though. You can see through the perf still from the inside, even where it's lighter. If it was a chunk of the liner, you'd think it would be solid and you wouldn't be able to see through the holes.
Also, I looked at the back of the glass multiple times during and after the install, and that spot wasn't there. It looked perfect. Now, it's pretty obvious from the inside, about eye level. The owner said it appeared about a week later... I walked in to talk to him about another sign, glanced at that window and noticed it immediately.
I did use some Rapid Remover to take some old adhesive off the window before the install. Then I thoroughly wiped down the window with Rapid Prep, then cleaned it once again with Rapid Tac. I wonder if some Rapid Remover made it through both cleanings and is eating up the adhesive under the vinyl? Also, I did have several bubbles and popped them by poking a hole in the laminate with a sharp Xacto, right in one of the perf holes. I noticed it appears as if it's running down from one perf hole and then spreading. Would it be possible for moisture to get in through a tiny hole in the lam and somehow harm the black? That doesn't make sense either though because I've done it without lam quite a few times and never had a problem.
Also, the discoloration follows the lines of holes, it's not just a random sized spot...
Like I said... I've done a lot of perf on vehicles and store-fronts and have never seen this.