It's not always easy to tell with this sort of thing without being able to open the module in the Toolset to see what's going on. But, the following are some possibilities you might want to double check. Obviously, it could be something else, too.
1) The item is in the store, but not on the page where you expect it. (This happens more than you might think.)
2) There are two stores in the area and the one being opened by the merchant dialog isn't the one you think. Or the store you expect to see doesn't have the tag the open script is looking for.
3) The item is in the template for the store, but not in the store itself. E.g. a custom store was created in the palette and then added to the module. But, the new items were added to the palette store.
4) The items are bugged somehow (bad portrait, string problem, etc.) and don't show up in-game.
5) A custom script is running for the store that is clearing some items out.
