Hello
I try to explain you how works URL builder in Zoo.
And I want to note that JBZoo uses same functions for building url as classical Zoo.
Did you try disable ZooSeo plugin ?
Usually, Zoo builds url for category as
(for custom menu item)
/<menu item alias>/
/<menu item alias>/category/<zoo subcategory>
/<menu item alias>/item/<zoo item>
if ZooSeo was enabled
/<menu item alias>/
/<menu item alias>/<subcategory>
/<menu item alias>/<zoo item>
Maybe you have for each category own item menu, so
/<menu item alias>/<sub item menu alias 1>/
/<menu item alias>/<sub item menu alias 2>/
...
I mean, that in this case aliases from zoo doesn't use, because all url builds by Joomla API only.
As result, I recomend you to use second way (if categories are not very much).
Please, can you tell me, what method did you use?