I'm not surprised that stores are discounting d20 stuff at wildly different times. The d20 explosion taught retailers that they have to make an effort to manage their RPG stock.
For instance, my FLGS only orders a few d20 lines, but they had to go through a process of ordering stuff and seeing what moved, and what didn't. When I lived in NYC, the FLGS I frequented there went through the same thing.
A lot of game stores have a shelf or so of Fast Forward stuff, and maybe another shelf or two, of books that are essentially dead stock. Luckily, RPGs are a much smaller investment than CCGs. I doubt many stores, if any, were in danger of going under because of it. The smart retailers figured out pretty quickly which companies failed to make sellable stuff and which ones made stuff that people wanted to buy.