Usually this is due to you missing a price table on the product in Netsuite. Our system sees this and stops the sync and moves on.
You need to define at least a base price. For product families or matrices in Netsuite you must assign a price to both the parent record AND the children products. Just use the lowest priced child product's price for the parent if you arent sure what to put. There just needs to be some value in the parent's price table.
Once you add a price table, our system will finish the sync and then you will see categories assigned as expected.