Good buys on booster packs at such locations seems common; besides the unfortunate instances of fake cards, the cost-of-materials and even shipping isn't too bad for a booster box. Some stores aren't sure if they'll sell well enough at full price, or don't realize the standard market up.
When Yu-Gi-Oh was on its second English set and boosters were $3.5-5 depending on location, a small town gas station about 20 minutes from where I lived had them for under $3... until I bought them out. Knowing they were in demand, they went up to MSRP and never came back down while I lived in that location.
In some cases it might be because "retail space" is at even more of a premium in such stores, and it isn't as easy for them to "clearance" older boosters - best to make sure they do sell easily.