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My best guess would be the visibility setting… you currently have it set to catalog instead of global.
I’m not 100% sure what the value would be (I would try global) but I import a large amount of products and I use MAGMI.
I would suggest taking a look at magmi and see its functionality, it provides the same import function as the native import tool, but much faster. The value in MAGMI would be 4, but as I said in your case try “global” or whatever you see on the back-end.
Head to your database and look in catalog_product_entity to see what they look like--compare them to the existing products. Make sure the entity_type_id, attribute_id and type_id settings are correct (errors here can make products not appear in the backend).