The majority of bookstore managers who determine stock levels will look at what books sold in there store, what books sold in nationwide trends (best seller lists) and will stock those.
Having worked at Borders HQ a while back, it's actually not the bookstore managers that even make that decision, but the team of Buyers at the corporate offices that decide how many of what gets ordered and sent where. (For the big chains, at least. Of course, local bookstores may be different.) At least back in the late 90's when I worked there (corporate tech support, so I fixed people's PCs all over the offices), I believe there was 1 guy who handled all role-playing, fantasy fiction, sci fi, and horror, too, I think. Obviously RPGs were a pretty minor part of his job compared to those other sections.
In the decade since, I'm sure it's changed somewhat, but I still seriously doubt that the hundreds of Borders managers, and thousands of Waldenbooks managers really have much individual say in what gets purchased. It's a combination of tons of sales data, and huge stacks of review copies of books.
When I was an employee there, it was always a good idea to get in good with the buyers, because they had literally boxes of books sitting outside their cubes free for the taking. I know it sounds fun getting an advance copy of pretty much every book released in your area of interest, but every day they had to alternate reviewing row after row of numbers, and quickly thumbing through a dozen or more books a day.
Now, this is just my guess from how I know their workload was before, but I'm figure that something like the PHB2, being in the RPG section from an established publisher, probably garnered maybe a half hour attention one afternoon to determine how many were ordered for all Borders and Waldenbook stores. After all, there was probably stacks and stacks of "the next great sci fi author" novels to sift through that day. Of course, if someone from WotC was pushy and tried directly courting more sales, that's a different story. Like I said, that's just my guess from seeing these people work almost a decade ago, so take it as you will.
But the big chain orders would be almost entirely dependent on a brief review of actual sales data appearing in some ugly report (they were still running it all off of a 20 year old pain in the butt mainframe up until '99 at least), and maybe or maybe not some sweet talking from WotC about how awesome this book is going to be (just like how awesome every book every publisher tries to sell to the stores).
Lastly, I'm not surprised if they are doing poorly. I could tell you some horror stories about how bad that place was run - especially around the sordid history of Borders.com.
