The term stock rotation refers to the rotating of shop goods after a set period of time. The amount of time for stock rotation is still unknown but is suggested to be around five minutes. Some people hate this feature in Oberin because it keeps them from selling their special craft virtually all day. Each shop has 2-3 different rotations.
Ways around the wait include trading to others (which is generally more profitable, once Shop prices are known), letting others store your extra merchandise for a fee (usually selling), and either filling your Bank Inventory (Command-N on any top step) or else someone's Guild Hall chest(s). Preferably with permission.