Except for a couple of Florida stores, these passes are not kept in stock at the stores as the demand doesn't warrant keeping them in stock. The stores order them, it takes up to two weeks to get them (although it can take as little as 2 days). What all stores get is the green exchange voucher.
DC and WDW have the capability to encode the basic information on the passes (name and address, etc), the stores do not, which is why you may get the character passes if you order them from those sources and you don't from the stores.
Purchasing the passes at the store doesn't impact their sales, because they are not considered store merchandise.
Unfortunately, because the stores and WDW are completely separate business divisions, they don't have accurate information about each other. For instance, guests have been told by the CRO office to bring passes into the
disney store to be returned. However, because the stores have no way of checking passes for days used, returns on all passes are prohibited. Guests also have been told that the Disney Stores sell all the hoppers that are sold in the parks, which is also not true. Finally, if you order passes and decide not to take them, that is your prerogative--they can be sent back.
Sorry that some people have had bad experiences. Just like anywhere, there are good employees and bad employees. People who are fully informed and people who don't care to know about anything more than the minimum needed to perform their job.
Hope this info is helpful.
Suzanne