Hi,
The module will only show the products that are related to the product bein displayed.
So if you only add two products as related products of a product, you'll only see two of them in the module even if you set that you can display up to three products in the related products module.
Wouldn't that be the explanation of what you're seeing ?
Otherwise, it could be that you've configured the module to not show out of stock products and some of the related products don't have stock.
Or you've configured the module to only display recently viewed products and thus you don't see in the module the products you've not seen recently ?