The faction stores are no longer buying items... or at least, that was the intent. I thought setting the purchase rate to 0 would fix that, but apparently, that's not the case. I'll have to go through them again and see if this can be corrected.
The reason for the change, in case anyone is wondering, is simple: we wanted the unwanted magic items to become more available and accessible to everyone so that they may spend their hard-earned coin rather than having the items hidden away and lost to private, exclusive shops reserved for the select or priveledged few. Besides, when you think about it, it didn't really make much sense for faction stores to buy back items for a higher price than most common shops when they would only be able to sell it to other faction members. The faction stores are meant to be outfitters, providing specialized and uniform equipment for their organization members at a reasonable cost. Most factions already have the benefit of better prices at most stores that support them. For example, most shops in Dagger Falls offer some discount to members of the Dagger Falls militia, while most shops in Teshwave cater to the Zhentarim factions.
As for the varying prices on potions and some other specific items, this is somewhat of a mystery to us. When the server was moved to the new machine, a number of things that were working fine with the mod on the original machine seemed to just fail despite finding any logical reason to do so. The healing kits, for example, was one. The altered dex bonuses for armors is another. Everything was copied over exactly as it was from one machine to the other, and yet, certain 'systems' in place are now no longer functioning. Personally, I do not know why or how the healing kits and potions were made to have a much lower price than their original value before, but until that little mystery is solved, we'll just have to accept some of the changes as they are. Call it inflation, call it the universe righting itself, call it unfair. For now, it is what it is. Its not a bug, but neither was it intentional.