Hi there,
Presta 1.7.6.4. I just stumbled upon probably the same problem. I import products from CSV. So here's no cell formatting. So far there is only one category associated to a product. When I put the category ID instead of a name - for example 1001, the imported product lands in a newly created 1001 category instead of the previously imported subcategory with an "1001" ID.
It should work like that (importing by category ID), doesn't it ? How else presta should know which subcategory the product belongs if there are many of the same name? They have to be same name for instance "mens" and "womens" for many main categories