Total Posts: 867
If you mean that the products are assigned to correct categories from admin, but not assigned to categories from the front-end, please, try to clear cache and to do re-index.
In case the products are not linked to correct categories from back-end as well as from front-end, then most likely it means that in the process of import category column was skipped.
Try to check the format of the file and data placement - you can export the file first and check how the products should assigned to categories and what format handles your import tool.
In order to check if this is the issue with your admin or some deeper one, as an alternative you can try to import via the application called Store Manager for Magento.
With this application there is no need to re-import again all the product data (since if I understood you correctly, the products were already uploaded, but not assigned to correct categories).
With Store Manager to link products to correct categories in the file you need to have only SKU for product identification and column with category. In this way it will take you less time, as it imports less columns.
There is 2-week free version of Store Manager, you can download it from th link in my signature.