I don know exactly why this fails. I only know that bulk uploading by csv is a very secure job. 1 small mistake and it will fail. I have good experience with the following product. Its a very complete data tool for prestashop. There is a 14 days free trial, but also the pricing is low and has a bunch of features:
https://www.getdatakick.com/
Besides that in backoffice in the productpage you can generate for every product in 1 step multiple combinations per product. This is a standard feature. So if you have 20 combinations you can select them in the productpage in backoffice at the combination tab. then hit generate button and id's are made automaticly. Ofcourse you first have to create the attributes in the attributes and features tab under catalogue. For example: create a color attribute with 10 colors and save them. You can also make more attributes and in the combination tab make a combination of more then 1 attribute. For example: Combine color and size, just select them and hit the generate button in the combination tab(product level) it will generate automaticly all the different combinations.