Everyweek the FLGS where I live gets a shipment of at least 2 or 3 PF core books, ditto for APG, 1 to 2 Beastiaries, lately 3 to 4o Beasitary 2s, and they ALL sell out in four days and repeat. They have NOT sold a D&D4e book beyond Tiles in two months. The owner and manager have told me this. I go there often.
I'm not saying this is the same across the country, just noting how its going here in my local Oregon area.
Does your owner and manager advertise one game and not the other?
How are they positioned and advertised in the store?
Is there games being hosted for one and not the other?
Are there sales or out-of-store ads for one and not the other?
I saw a LGS (wouldn't call it friendly!) about a month ago that bragged about how 4e didn't sell, and in the same breath said he'd warn his customers away from 4e. Wow, what a shocker they didn't buy it!
Also he went out of business last week, so that worked out well for him!