I had an experience with John 3:16 as well.
The Canon EF-S 55-250mm was given a wrong warranty card, one that differs from the box and lens serial number.
Didn't notice until I wanted to registered for Canon's warranty. Went back and one of the guy practically searched through an entire file of warranty cards.
Apparently, they keep tons of warranty card. I don't know why but my original one must have been placed in some other box that was sold.
Awaiting a replaced warranty card from Canon, requested through John 3:16.
Whether it's a reputable shop or not, make sure you check the lens, check the warranty card serial number, check the serial number on the box.
Sometimes it might not be the fault of John 3:16 cause they will take stocks from AP or other nearby shops just to seal a deal. Sometimes it might be a human error as John 3:16 allows testing of equipment and the shop can get really messy. In any case, I won't be buying new stuff from them unless it's bags or small acessories. Looking at the number of hands molesting their new on the shelf equipment is rather daunting to me.