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Why does GetStore not return the same Store Categories that I see on my Stores web page?
What you see on the stores page depends on how you have set the display of the page. If you choose to display the Categories, based on eBay Categories rather than your Custom categories, then you will see the eBay categories for which you have items listed, rather than your own custom categories. However GetStore will always return the Custom Categories that you create for your store.
Here is an example of what you will see on the stores page, if you choose you display eBay Categories:
You can set the display of the categories on your stores page from My eBay > Manage My Store > Display Settings. Irrespective of how you set the display, GetStore will always return your custom store categories.